commit 88febc3330494e659affc64e6d1805eb3c5ef5eb
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Fri Mar 8 11:11:31 2013 -0500

    Updated AUTHORS file

commit cbc28ac7ad5de085c3b86204aae5c65b9e46f5b8
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Fri Mar 8 11:09:02 2013 -0500

    Updated 2D models to contain resolution for all models

commit 91124effdf5078dc69cb8c49f8e97abb5295c001
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 8 00:35:29 2013 -0500

    Updated method so that the default metadata for training a 2D model is similar to a 3D model

commit 4409faf41356cb6bfc2936c1de24e8d239920f11
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 8 00:34:56 2013 -0500

    Updated method so that figures are dependent on the display flag

commit 6bf2f8030098d7ec64e47e2416e473c627060e31
Merge: 5dc0e80 35836b7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 7 16:53:16 2013 -0500

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 5dc0e805c62242dab2140a634827351670cb2323
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 7 16:52:04 2013 -0500

    Updated method so that if the distance vectors in the cell codes structure are not of
    size 360, it ignores that image for training the ratio model

commit 35836b76cb8054ca3398c651ed59ad6f4f558bc0
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 7 11:42:48 2013 -0500

    Removed bug from demo that was using the wrong url to download the data tarball

commit 22e6d1bd9f5e885e9e63a40336f0d5cfcaac976b
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Mar 6 23:05:39 2013 -0500

    Updated demo2D01 to use built in methods for downloading files and decompressing tarballs

commit 1d389a807b8c17c66b7a663720df32149735cf17
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Mar 6 19:29:32 2013 -0500

    Updated message in microtubule synthesis code

commit 96b353d2926a5bc215acd123a28f5f9fdea5a81c
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Mar 6 19:23:13 2013 -0500

    Removed error from method when checking the existence of nuclear instance

commit a46d0fc0010374931cb899b18294235ed56123b8
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Mar 6 19:21:55 2013 -0500

    Removed interactive message that displays generation of objects from protein pattern

commit 31be5b876b83c09fb068dcac499fc40c1d056374
Author: Devin <devins@cmu.edu>
Date:   Wed Mar 6 15:02:08 2013 -0500

    changed default protein model in diffeomorphic model to lamp2 pattern

commit 886228d85b79d9d4ed9ebcbc386d7a3c6a990063
Author: Devin <devins@cmu.edu>
Date:   Wed Mar 6 14:55:51 2013 -0500

    fixed resolution tracking for demo3D17, added resolution param structures to both demo3D16 and 17.

commit 140fb9d646581be38a9da3a0c83ffc53a1434537
Author: Devin <devins@cmu.edu>
Date:   Tue Mar 5 17:36:28 2013 -0500

    added code to handle premade/pre-segmented frameworks in model2framework and fixed demo3D16 so that it does the downsampling properly (speeds up demo considerably)

commit a4e1c633e85fa95ab93cb1903530dc7d32daf263
Author: Devin <devins@cmu.edu>
Date:   Tue Mar 5 14:25:07 2013 -0500

    fixed minor bug in resolution handling that was treating resizing of nucleus as equal for all dimensions (this is not true in the microtubule models)

commit ace50d62e56e6369d1f8e3b75bfd308239099d4f
Author: Devin <devins@cmu.edu>
Date:   Mon Mar 4 15:21:46 2013 -0500

    Corrected param.downsample in demo. Downsample is the number of times you wish to downsample the image and so should be >1. Corrected code sets param.downsample = 5; If a downsampling of less than 1 is specified the program will ignore downsampling and attempt to generate a mesh at the full resolution of the images.

commit e85668b05e23e6eada20ade50e54418b55f6002b
Author: Devin <devins@cmu.edu>
Date:   Mon Mar 4 15:18:40 2013 -0500

    Fixed 2D demo to assign outres when synthesizing an instance

commit c5320ce07f0c37c6496060b87eb1e3aefd23f583
Merge: a0ee72a 5a04e1f
Author: Devin <devins@cmu.edu>
Date:   Mon Mar 4 15:07:04 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit a0ee72aa5fecdbf5ee32152b03c9dbd3e4d18682
Author: Devin <devins@cmu.edu>
Date:   Sun Mar 3 21:10:07 2013 -0500

    fixed 2D synthesis by setting outres in model2framework

commit 5a04e1f9a004e4c4e7b6fe583cb6f3fa134d8ebd
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Sat Mar 2 19:51:13 2013 -0500

    Removed temporary files left after last commit

commit 6a1dd849d15386d82ac147b59bccc2c83a4832af
Author: Greg <greg@Gregs-iMac.local>
Date:   Fri Mar 1 16:10:58 2013 -0500

    updated ml_rcthreshold for arbitrary bitdepth

commit 66c89cbb01b8ec23fb3a61676df54c8bc4642f6b
Author: Greg <greg@Gregs-iMac.local>
Date:   Fri Mar 1 16:07:50 2013 -0500

    crop image function

commit c07f46442ab49e5ac8feee5d21c94479ab6e65f3
Author: Greg <greg@Gregs-iMac.local>
Date:   Fri Mar 1 12:57:22 2013 -0500

    Updated to hole-finding code

commit 69d165eeb99d7e95c2cdbc08ce06856d012fa359
Author: Devin <devins@cmu.edu>
Date:   Wed Feb 27 18:31:03 2013 -0500

    fixed resizing stuff for MT model and commented other changes

commit 1c1fa476a37ca69629436ec5f8d101b1dae0c630
Author: Devin <devins@cmu.edu>
Date:   Wed Feb 27 18:16:04 2013 -0500

    fixed MT model resolution and centrosome placement models

commit b21eadcc15c2540019d84f3e00f7a4def590d037
Author: Devin <devins@cmu.edu>
Date:   Tue Feb 26 18:53:47 2013 -0500

    fixed small bug in resolution saving

commit 10546db137cce372f4942ee0d6f9e3f3a235de58
Author: Devin <devins@cmu.edu>
Date:   Tue Feb 26 18:01:01 2013 -0500

    manually adjusted model resolutions based on the new information from the training code.

commit 09634ed589b60aa1e1f40b4c2f458bb20aced7c7
Author: Devin <devins@cmu.edu>
Date:   Tue Feb 26 17:58:57 2013 -0500

    Fixed small bug in code to not try to resize from param.resolution.objects if the model is 'centrosome'

commit ba75c84d539b83ccd3adf6d08b1b3b83c1c1c21d
Author: Devin <devins@cmu.edu>
Date:   Tue Feb 26 17:53:14 2013 -0500

    fixed bug in training introduced by me on Feb  24

commit aec300f51de0664c59d22aa2933a8003050c2bd8
Author: Devin <devins@cmu.edu>
Date:   Sun Feb 24 16:14:16 2013 -0500

    revert to multiplying trained models by a constant, instead of being fixed at 5, user specified by param.model.proteinUpsampleZ and track resolution/downsampling correctly.

commit 58c6e71bcf77339032cbbd39154e1104fc5a296d
Author: Devin <devins@cmu.edu>
Date:   Sat Feb 23 12:45:50 2013 -0500

    training resolution fixes

commit 9933053fa664c42280376b3da7cee5de5da51e99
Author: Devin <devins@cmu.edu>
Date:   Fri Feb 22 18:47:37 2013 -0500

    Makes framework synthesis dependent on vesicular resolution (assuming cubic voxels)

commit 3da0973b41a7b43201ba5cc085cf5a3037e6d049
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Feb 22 11:43:20 2013 -0500

    Updated methods so that users can pass in a downsampling vector from the main method, img2slml

commit c59242a7126333d3828ece2dddace2bfada3a4a9
Author: Devin <devins@cmu.edu>
Date:   Thu Feb 21 17:05:15 2013 -0500

    fixed minor bug in last update

commit 8b521b61f0a28d52a1e50aa80bed82210cc9da52
Author: Devin <devins@cmu.edu>
Date:   Thu Feb 21 16:28:58 2013 -0500

    added cosmetic changes, ability for user to manually specify resolution, overriding the model specified resolutions while printing a warning to the user

commit 3a7aca5f4eaa96e887985ee6fa533dfb6dccc10d
Merge: 0e45bfc 94c5ddc
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Feb 21 10:03:21 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 0e45bfc3460f3a4165d43e4b61f0d0340ce210c3
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Thu Feb 21 10:01:22 2013 -0500

    Greedy3D_lambda_pre_compressed.m can now be called with option lambdas_are_distances_from_source = true to give distances to interpolate instead of lambdas for argument lambda_list (use of negative values to indicate distances is now deprecated), which works along with options known_distance, the approximate distance between source and target, and stop_source_distance, the maximum distance the source has to travel during integration (respectively (known_distance - stop_source_distance) for the target).
    compute_shape_space_model_given_images.m takes computes a shape space from input images.
    generate_frame_from_trained_shape_space_model.m synthesizes a shape for a position in a shape space.

commit 94c5ddcdb997fc1e214ad1f8cc349c40a8735c88
Author: Devin <devins@cmu.edu>
Date:   Wed Feb 20 18:52:49 2013 -0500

    fixed resolution extraction from models

commit c0e5a96535ea4b155685fb626e6b6e1f7adb8680
Author: Devin <devins@cmu.edu>
Date:   Wed Feb 20 17:16:03 2013 -0500

    fixed bug which forced all multi-resolution images to produce binary images. this broke the 'sampled' mode.

commit 8158f0003f53796b75e0e730b010b18a493c5d73
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Wed Feb 20 12:45:21 2013 -0500

    Allows odd-sized A as well as B by the same mechanism

commit 93acddf7b2257a5a176cbd111ea5e3cf95fd6a56
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Feb 20 12:34:30 2013 -0500

    Changed relative directory path to be compatible with MacOSX and Linux systems

commit 9475444f5248df30942339c9a23843f3eaea41ce
Merge: ab7d052 0c7d327
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Feb 7 10:01:15 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit ab7d0522992f9b0aebd48e5626991ec97b05269d
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Feb 7 10:01:05 2013 -0500

    Updated code so that during training a user is forced to input the resolution of the training dataset. The code then uses the downsampling vector and the resolution to calculate the resolution of the model and saves it to disk along the rest of the model

commit d7e9c2386a18b23b6fdf715e1967f4a50e17dea8
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Feb 7 09:27:24 2013 -0500

    Fixed small typo that was introducing a bug

commit 328ca95ea5f4a800b40f97d89e32e57925175666
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Feb 7 00:12:23 2013 -0500

    Updated demo3D12 to include the resolution of the 3D HeLa dataset

commit 0c7d3271d73068c2b8c66d207ed7e03e865c0864
Author: Devin <devins@cmu.edu>
Date:   Wed Feb 6 20:19:55 2013 -0500

    Return synthesized resolutions and modified MT code to work with multiple resolutions. Need to double check that this will work for the 'sampled' method

commit 7810fd7c4199a04c6c9c1a1a01157928d8e9fed4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jan 30 20:48:39 2013 -0500

    Plots will be shown iff display flag is set to true

commit 2d55371063b8ae03f13546117a9c3bfb3c520372
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jan 30 20:47:26 2013 -0500

    Removed old documentation from method

commit f4458449561eafdd626341c2669be3678594712a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jan 30 20:37:21 2013 -0500

    Updated methods to use print displays according to verbose flag

commit 3bdcdcb884e77d2cf671a5d3acb7b8c3b29cadff
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 15:47:50 2013 -0500

    Made declaration of temporary folder, platform and opeerating system independent

commit 5ad05176958e96ec372c7572076572f425753365
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 15:38:48 2013 -0500

    Display of plots in this method will happen if debug and display flags are both set to true

commit e5489492e1cd150ceb6936a96a80f5453c98d735
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 13:51:45 2013 -0500

    Updated method so that if decompressed folder is found, then it skips decompression of the images tarball

commit a339fdeed4e7feff2d55ce31aca977675dab3b74
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 13:38:34 2013 -0500

    Updated code so that parameter isshow is always set to false

commit 1ff5b91efc6f3c94d38b0e3fda2b4639c0fa0328
Merge: 829868a 1eb653a
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 13:32:06 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 1eb653a87b694a66d9c431ec35907ff07e0d97be
Merge: 49b77e6 4980bb9
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Wed Jan 30 13:28:37 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 829868a03a802ec4e3c3f724f8fd6742d7ea1855
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Mon Jan 28 13:12:18 2013 -0500

    Updated method so that models are saved as mat files instead of XML models

commit 4980bb9cb85e5dcf009b309b3137bedea3e4c1f1
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Mon Jan 28 12:29:07 2013 -0500

    Updated try/catch statements to print a detailed report when running debug mode

commit ead3c93ff4dd6d17e54e6e451f00c2563b8b55b9
Author: Devin <devins@cmu.edu>
Date:   Fri Jan 25 13:15:53 2013 -0500

    Added uint16 capabilities to ml_rcthreshold.m

commit 49b77e6d016e9dd9581e6021977c8c0e9e640fc0
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Fri Jan 25 11:28:38 2013 -0500

    Fixed bug in the interactive version of demo3D12

commit d880071149b7a6e7711e6dce220a9928c33a1a15
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Fri Jan 25 11:28:12 2013 -0500

    Updated demo3D11 to reflect latest changes in CellOrganizer

commit bb89d9711588d9597ddd940561603795552cc719
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jan 22 17:26:10 2013 -0500

    Modify method so that it extracts resolution information from first model in the list of models

commit 7d36fcb6fc7b429d05fb3e83c9e32ea257be8262
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jan 22 16:44:04 2013 -0500

    Modified if statement so that it checks whether resolution exists in parameter structure before querying it

commit e48b29ae68ebc768e994ec88fb8f552c6eaff8c3
Merge: 24ea440 ab22da5
Author: Devin <devins@cmu.edu>
Date:   Tue Jan 22 09:42:11 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 24ea440e0363ce3bcd0a9f8c9cb3f1c892839215
Author: Devin <devins@cmu.edu>
Date:   Mon Jan 21 20:59:39 2013 -0500

    Changed resolution handling, added psf resolution, added contrast stretching to img2tif

commit ab22da57c3187470744e68137b14e5a9605dfd83
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 17:17:19 2013 -0500

    Fixed bug in diffeomorphic instance synthesis were the parameters of CellOrganizer didn't match the newly trained model

commit b88a7d67eb520ff034554c8864b86dcee8688472
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 16:23:13 2013 -0500

    Updated correct version of the diffeomorphic model of the cell

commit d90ff39320d01a10b1f446cb5455098f6e50671d
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 15:49:40 2013 -0500

    Updated model files with resolution of all the submodels

commit 5849a23b8722d00b3fc6a53709e7f8e17feccc18
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 15:42:10 2013 -0500

    Updated demo3D17 to look for the synthetic examples in the images folder

commit a8512cab551741d15d5425d289643f20c2d400b8
Merge: 0f87939 35c8425
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 15:08:12 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 35c84259d8f298ee8df98e272342c05fa96aaffd
Merge: c70b26d 33882da
Author: Devin <devins@cmu.edu>
Date:   Mon Jan 21 15:07:05 2013 -0500

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit c70b26d6f5f759b91bb8210e0a9c3f1792b082b6
Author: Devin <devins@cmu.edu>
Date:   Mon Jan 21 15:04:21 2013 -0500

    Changed param.resolution to allow for a single specified model resolution for all object models or individual object models

commit 0f879399eadf7356146218fc6812dd78e1e55bef
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 14:54:11 2013 -0500

    Put construction of the object document model and the parsing of the XML file into two separate try/catch statements

commit 16b504020bd62300faf5b398587d08bb2a111cf2
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 14:52:51 2013 -0500

    Removed examples from documentation header

commit 79fb40bff1070872ad9f970c2cf3917c8da3da3c
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 14:52:03 2013 -0500

    Updated trainer to switch UI whe switching dimensionalities

commit 30cf6bd6c3a845500e227147f7cf3114825d8a85
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 21 13:55:18 2013 -0500

    Updated diffeomorphic model file

commit 1489e018cc4b4c78e5e0cc2f56117efbeaddeb5b
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jan 17 09:12:50 2013 -0500

    Removed check of jpg files from helper script

commit fb049b6aedecdb7cb1600618a19f450d1da2cbb3
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 14 17:09:15 2013 -0500

    Debugged and tested the trainer tool for training 3D models

commit dcacb5bd5eb7eebd6c180d2365dd0900db84bf69
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 14 11:34:09 2013 -0500

    Removed bug in Reset button method that tried to clear nonexisting fields from the GUI

commit 60542fef90f8bb3026edee3415b9cedc377e930b
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 14 11:23:52 2013 -0500

    Removed version number from splash screen

commit 073650800ff79f83eaa9116cf1e2e699dcddd4ac
Author: Ivan Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jan 14 11:23:18 2013 -0500

    Updated version number for next release to 1.8

commit 33882da7453f1639e3b76987bc905158d9fecf05
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Dec 5 01:33:32 2012 -0500

    Removed demo3D15_nowindow_downsampling_scale2_abserrstop test

commit 8d7832b4fe242ec9306bcc4c2a520d4aea32ff9a
Merge: 00d3fcd 788c49b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Dec 5 01:30:02 2012 -0500

    Merge branch 'dev' of git@bitbucket.org:icaoberg/cellorganizer into dev

commit 00d3fcd396eccb3bed01a842c50c21c03926ad89
Author: Yue Yu <yuey1@andrew.cmu.edu>
Date:   Wed Nov 28 17:12:26 2012 -0500

    Added absolute error convergence criterion option to Greedy3D_integration_compressed called convergence_absolute_error. Added an option to synthesize shapes with downsampling in the XY plane to make it faster.Changed demo3D15, generate_frame_from_trained_shape_space_model, etc. to use both of the above features.

commit 788c49b5f3c3d1a86160d4334ae396c1f939680e
Author: Yue Yu <yuey1@lanec1.compbio.cs.cmu.edu>
Date:   Wed Nov 28 17:12:26 2012 -0500

    Added absolute error convergence criterion option to Greedy3D_integration_compressed called convergence_absolute_error. Added an option to synthesize shapes with downsampling in the XY plane to make it faster.Changed demo3D15, generate_frame_from_trained_shape_space_model, etc. to use both of the above features.

commit 1a5d30bfcbe89731b1e2d598586f669c681b087c
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Mon Nov 26 13:52:48 2012 -0500

    Removed debugging statement left behind by previous commit

commit deee4635477d6dfef17e708b3a977b7903379369
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Mon Nov 26 13:42:10 2012 -0500

    Included downsampling scale to parameter structure for the synthesis of instances from diffeomorphic models

commit 036ebbfc7445a84eba25c4b302611191a8687255
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Sun Nov 25 17:32:52 2012 -0500

    Included the maximum deformation per step to model2framework and removed a bug that was setting the maximum iterations to 2

commit 15cadca6cdd0b4509d1945261612176f4a0cb947
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Nov 16 17:45:10 2012 -0500

    Updated and cleaned code of demo3D11

commit e9c3df5f525d83612ebda24a7655f6696d53acec
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Nov 16 12:19:55 2012 -0500

    Updated code so that parameter structure can be passed to model2framework to allow model2diffeomorphic to inherit parameter values from slml2img

commit 983ad617fbe1916c6fccfca45c763737a1c1db78
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 17:23:32 2012 -0500

    Updated demos so that they clear parameter structure rather than clearing all variables in workspace

commit 7a67a4f052a6c7a995aa1c73fa9868551e86752f
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 17:21:38 2012 -0500

    Tentative update of diffeomorphic instances generation

commit 9ee277f35542613d6d3263226327e6ca053a1cc9
Merge: 692d621 bc281b6
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 16:59:31 2012 -0500

    Changed warning to display message

commit 692d6214bcbeb5892e9ca155830ba122dfe56648
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 16:58:00 2012 -0500

    Added license and updated messages to command line

commit e0fe45c94ec4f88c8a95bab4e2baaad4156e0367
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 16:42:08 2012 -0500

    Changed warning to regular display

commit 65ee64cace1b3d83ba6e5d0debf58595398d2f68
Author: Ivan E. Cao-Berg <icaoberg@scs.cmu.edu>
Date:   Thu Nov 15 15:22:55 2012 -0500

    Changed warning to regular display

commit baa553a95e6ec5a4c3eb8fba794464bbd739b00b
Author: Devin <devins@cmu.edu>
Date:   Wed Nov 14 12:07:00 2012 -0500

    Fixed the resolution adjustment in model2instance. Required rewriting param.nucleardist and param.celldist as well as param.nucleus
    and param.cell in addition to the read in 'nucleus' and 'cellMembrane' images which seem to be unnecessary copies of the
    param.nucleus and param.cell images respectively.

commit bc281b6ae7e5d2b08915e499046b9f6451025d34
Author: Devin <devins@cmu.edu>
Date:   Wed Nov 14 12:07:00 2012 -0500

    fixed the resolution adjustment in model2instance. required rewriting param.nucleardist and param.celldist as well as param.nucleus and param.cell in addition to the read in 'nucleus' and 'cellMembrane' images which seem to be unnecessary copies of the param.nucleus and param.cell images respectively.

commit 458a25ea5c63c81289a274555ff0eade8cff1e80
Author: Devin Sullivan <devins@cmu.edu>
Date:   Tue Nov 13 13:15:15 2012 -0500

    Included resolution parameter that allows the user to input the cell framework resolution and the output resolution of the protein images so that synthesis occurs at the same resolution

commit e102b9913f66d4a5ea1cb55a47773dd0ff78427f
Merge: c8df373 b962ddc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 12 13:39:47 2012 -0500

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit b962ddc01d5a1806faf219433d6a51086626378d
Author: Devin <devins@cmu.edu>
Date:   Fri Nov 9 15:50:54 2012 -0500

    adding smaller .obj files rather than the really large ones

commit c8df37324e7df8f5a63add6eacf09b4a3fea0f6d
Merge: e01f7b8 367595f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Nov 9 15:46:50 2012 -0500

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 367595ffbe8c62d9796412dc401203a4fe6f9621
Author: Devin <devins@cmu.edu>
Date:   Fri Nov 9 15:45:32 2012 -0500

    Improved im2blender.m to include a reducepatch call which downsamples the number of verticies in the mesh. This makes the .obj file much smaller. Also added the amount of reduction to the inputs for im2blender and created a default catch of 0.05(5% of the original image verticies are kept) which I found to be suitable by visual inspection in Blender. Cosmetic changes to demo3D10.m.

commit f479590b30787d69f322d5d964dd800801debf7a
Author: Devin <devins@cmu.edu>
Date:   Fri Nov 9 15:41:45 2012 -0500

    Fixed bug in img2slml.m, model.cellShapeModel.type was being set wrong

commit e01f7b87c30427343b521d71ed92dbc9b9359a5c
Merge: 3c7c2bd 7b44500
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Nov 9 15:37:41 2012 -0500

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 7b44500907d1c04a03a67d3115f1748b4d4f4f35
Author: Devin <devins@cmu.edu>
Date:   Fri Nov 9 15:24:29 2012 -0500

    Fixed bug in img2slml.m, model.cellShapeModel.type was being set wrong

commit 3c7c2bd07bbc3af3cdddd91e55e112e6eeadf379
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 8 13:58:51 2012 -0500

    Changed location of test image for demo3D16 to a permanent location at the root directory so that it can be shared by multiple demos without being associated with particular one

commit 17c9933fcf4cab3f46291d00a63549696069fb2a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 8 10:28:25 2012 -0500

    Updated method to make call to convnfft_fast rather than convnfft_faster

commit 5c82b6db4314af56fa1968c47f4c0d45fd80f13d
Merge: 8983171 05804a4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 8 10:13:58 2012 -0500

    Fixing automerge conflicts

commit 8983171f7e4174a3a7df1acab48268a13180a0b7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 8 10:02:39 2012 -0500

    Removed old copy of convnfft_fast

commit 05804a49ddf49f16e91fbb7d549093f986305ba2
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 8 09:55:37 2012 -0500

    Renamed convnfft_faster to convnfft_fast

commit a6bed090cdcbea6b36964676bb01551255f3162f
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Thu Nov 8 09:36:35 2012 -0500

    Modified methods to use convnfft_faster rather than convnfft_fast

commit c51a317a355e8b0469eebba38b970f23e32f2faf
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Thu Nov 8 09:26:28 2012 -0500

    Optimized faster version of convnfft_fast

commit ffd27def18ba4affee7e7797623e24f50fb0f51f
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Tue Nov 6 10:46:00 2012 -0500

    Updated synthesis code to use Euler integrator

commit 48a4f5f7150081538a6805c3b3b28df834ed5126
Merge: 953a376 f67daff
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 5 14:16:44 2012 -0500

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 953a3767835a263be51978a62a7c9c5171e8a481
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 5 14:14:30 2012 -0500

    Updated demoinfo file to include demo3D17

commit f67daffc8eb80e5f0ed5c052abea7db20508109e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 5 14:14:30 2012 -0500

    update demoinfo file to include demo3D17

commit 409fd1563a2c01a1c15f7f7d111f321a651cf820
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 5 14:12:01 2012 -0500

    Included basic template for demo3D17. Needs inclusion of param.resolution

commit 2a6bc3cee51ede981e14928936956ff8411c2540
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Nov 5 12:35:20 2012 -0500

    Included synthesized images for demo3D16

commit 59dcddc774cbfba0a4266da20ea9ca524bd7eb21
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 1 18:08:38 2012 -0400

    Update demoinfo file

commit b04e1ddf3e9ec5353679b6c6f1f7eb35ed43b11c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 1 18:07:54 2012 -0400

    Included demo3D16, which synthesizes an protein pattern for a framework given as input by the user. This demo is meant to show the new functionality at which a user can input a framework to slml2img

commit 99b61b6cde2d002d8186ca78d2ea6f8d9348b929
Merge: ae8a654 257b557
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 1 17:18:20 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit ae8a654fd18dfafcc9fe2464771690c18f17c157
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Nov 1 17:17:37 2012 -0400

    Included synthesis method selection to parameter structure that allows the user to specify whether to use convnfft or convnfft_fast when synthesizing instances from diffeomorphic models. Even though this option is accessible from slml2img, it has purposely not documented due to the fact that at this point is meant for testing purposes

commit dd8d83555feca383f344b5cb0e7a8c5c43bacdb4
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Thu Nov 1 17:09:27 2012 -0400

    Included an alternative implementation to convnfft

commit 257b5578cb6482954976ad286ab23425bc784624
Author: Devin <devins@cmu.edu>
Date:   Thu Nov 1 13:33:12 2012 -0400

    Fixed comments that had become uncommented somehow and caused code to crash

commit a565d4f46b1ccda5fb3fe40ae90114f77ea0a327
Merge: fb4ec03 a8feb98
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Oct 31 12:00:11 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit a8feb98235951263879b2c0b5df817b6bba4edf0
Author: Devin <devins@cmu.edu>
Date:   Mon Oct 29 16:01:23 2012 -0400

    Fixed bug in im2blender.m, decreased isosurface threshold to detect boolean objects

commit fb4ec03519290832ece57e2468fd4c36255d726b
Merge: d7ebe26 4eab2f8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Oct 24 19:06:09 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit d7ebe265b596e9ca7635182d8cf4043dacc0e7cd
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Oct 24 19:05:48 2012 -0400

    Modified convnfft to call ifftn rather than iterating through all dimensions using ifft

commit 4eab2f8c7ec154f7c44d989ddcd142b9814405c0
Author: yuey1 <yuey1@andrew.cmu.edu>
Date:   Wed Oct 24 18:54:25 2012 -0400

    Moved Greedy3D_integration_compressed folder into temp folder

commit 61d698e9e4fc09dc4b76226575707185500f335a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 23 11:06:07 2012 -0400

    Updated demo3D15 to include option that only synthesizes the framework from the model it calls

commit a4edda53e47078093a790f18284587e589feb46d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 23 10:55:20 2012 -0400

    Included mex file for inplaceprod.c for MacOSX

commit 84d4a8935775aa574ae07cc2f065f828f7f72a02
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 22 15:30:00 2012 -0400

    Updated CHANGELOG to old format

commit 2ae73abb45e2b6098322afdf314f3721315976dc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 22 15:27:57 2012 -0400

    Added Matlab 3D figure to 3D (X)HTML. This function FIGURE2XHTML converts the 3D objects of a Matlab figure to an in XHTML
    embedded X3D file. In a modern browser, you can then view your figure interactively because of the great X3DOM Library.
    
    http://www.mathworks.com/matlabcentral/fileexchange/32207-matlab-3d-figure-to-3d-xhtml

commit c479f36274e65882252e5ceca4eb04fcb2fe34ca
Author: yuey1 <yuey1@andrew.cmu.edu>
Date:   Fri Oct 12 16:27:30 2012 -0400

    Added a method to create a 3d sphere image to test nucimg2nucsurf, fixed a interpolation bug in nucimg2nucsurf.m

commit 1a0072ad002e085aa2961230f36a6d6f1b2a582f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Oct 12 14:18:02 2012 -0400

    Documented method, added check of input arguments, encapsulated method in try/catch method so that method returns empty array if it fails

commit f0157255b44a6bfdbce36e8ac2287fcd9cb449ab
Author: yuey1 <yuey1@andrew.cmu.edu>
Date:   Wed Oct 10 18:10:42 2012 -0400

    Added a method to generate nucleus surface from nucleus image

commit bceac442add5e0e04bb438a0049eb40292038a6c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 9 17:04:06 2012 -0400

    Added new functionality to CellOrganizer that allows the user to decide to
    synthesize a nuclear instance, a cell instance, a framework instance or
    all. The default value is all, which mimics the previous functionality of
    CellOrganizer. This was added in request from other developers who are
    using this toolkit.

commit 987d5d1cb4b716cd741dddef11d8e6c7c832b808
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 8 14:37:35 2012 -0400

    Included demo3D15, which synthesizes a framework from a diffeomorphic model

commit 3075c96c97e3ef91cdac7221d0b3e32bcf5df0ba
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 8 14:35:45 2012 -0400

    Updated model2img to stop the synthesis process if the nuclear or cell synthetic images are returned empty from model2framework

commit 8ab310199358946d8473b70ee2268f6354455c8b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 8 14:34:03 2012 -0400

    Updated model2framework to include a switch which considers the synthesis of instances from diffeomorphic models

commit 72fd978ef2be40bda872ae082b9a0b51fbfbc9f0
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Wed Oct 3 15:29:08 2012 -0400

    Updated LDDMM distance to work on 3D images by replacing mean2 with three calls to mean

commit 73ace3b0e7fa059d5c996476001c0d055014e418
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Oct 3 14:46:14 2012 -0400

    Updated diffeomorphic model file

commit 05b91972916705ac94c5e79f3adbd15d45605237
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 2 11:17:34 2012 -0400

    Added GPL license for CellOrganizer to the licenses folder

commit eda10e02209c1971dfd1e1af3e33018ff55e35d7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 2 11:17:03 2012 -0400

    Fixed a bug in setup.m that would throw a warning when it tried to removed the licenses folder from the working path due to the fact that it was never added to path in the first place

commit 46a8928b454c44fcb3a72d94630ccfad16d295a1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 2 01:22:17 2012 -0400

    Removed cvs directories from this repository that correspond to the additional packages used by CellOrganizer. Online copies of all of the original packages can be found in the online repository

commit 1f8c7d10f600123f00e69c57e85f8151bc44459c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Oct 2 01:18:22 2012 -0400

    Moved all licenses to a common folder in the top directory and then added a line to setup.m that ignores this folder when recursively adding all folders to the working path

commit 9b25108e57da261f60aaf9c6b50bbc8e8fa85bc6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 1 19:10:50 2012 -0400

    Added scripts to synthesize images using diffeomorphic models. The current update does not work on Windows 7 x64, and will test in Linux

commit 705c19706afd9de65807f543cd6b1d5f19e888a2
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 1 16:36:00 2012 -0400

    Removed deprecated code from previous versions

commit 7986f6f257633d9aa669959ae5af05b32aad3bc3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 1 16:22:15 2012 -0400

    Updated code so that if model2framework fails to make a framework and
    returns an empty array, then this method returns an empty cell array as
    well as throwing a warning if the flag is true

commit ed979e006e48085bd2f7bd29040cc7147ea71c74
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Oct 1 16:14:48 2012 -0400

    Added diffeomorphic model structure so that the method knows what to do when a model of this type is added. I also added a default value so that if the model type is not recognized, the method returns empty nuclear and cell images

commit d9bf2449eaba84ba554e29aee8c9d209378cc006
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 28 15:42:10 2012 -0400

    Fixed a bug in the existing models. The cell shape model type was set to 'medial axis' and it should have been set to 'ratio'

commit 1ae8f07f7b7a68d16433658f05004254ddb81bfb
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 28 13:39:52 2012 -0400

    Added temporary 3D diffeomorphic models used to synthesize images. These models are temporary in the sense that they are the original files used by Taraz Buck in his code. Eventually this models will be turned into compliant SLML instances

commit fcf959f65f0a22dbe03f376532e0cf06e27ab228
Author: Taraz Buck <tebuck@cmu.edu>
Date:   Fri Sep 28 12:17:51 2012 -0400

    Included main methods for generating 3D frameworks using diffeomorphic models. This code does not include training of the model, only the synthesis side

commit 6b6604c07392dc41cd97a4e1aa450f907ea74ec9
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 28 12:04:07 2012 -0400

    Included 3D deformation code originally written by Wein by Wei Wang. This code calculates the distance matrix for the diffeomorphic project

commit b0ee50460b781405b7355ee6393da05040570ab0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 16:33:53 2012 -0400

    Efficient test for points inside a convex hull in n dimensions
    
    http://www.mathworks.com/matlabcentral/fileexchange/10226-inhull

commit 0ef9b3aca2a9b23b7215ea84af951b3dbb384aa3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 16:32:33 2012 -0400

    Exports figures nicely to a number of vector and bitmap formats
    
    http://www.mathworks.com/matlabcentral/fileexchange/23629-exportfig

commit 708db0809ee0e744f68d9929a3501e1e4dc9fa1f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 16:28:49 2012 -0400

    MD5 or SHA hash for array, struct, cell or file
    
    http://www.mathworks.com/matlabcentral/fileexchange/31272-datahash

commit acdf78b72cfe0eb6631a46b716cbd44575823fac
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 16:27:21 2012 -0400

    Compress Matlab variables in the workspace
    
    http://www.mathworks.com/matlabcentral/fileexchange/25656-compression-routines

commit f5ff5f130b6b07e8d502a7cd3c1f0c820ce9074d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 16:24:10 2012 -0400

    Discrete convolution using FFT method
    
    http://www.mathworks.com/matlabcentral/fileexchange/24504-fft-based-convolution

commit f56e4c1472a45d9a6825a5cd7dcd807805ed6f8f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 15:50:05 2012 -0400

    Added a package that integrates systems of differential equations until
    stability is reached (or time is over)
    
    http://www.mathworks.com/matlabcentral/fileexchange/25201

commit 168cb2979288338f566d41cfbb720bcaff38010c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Sep 7 13:53:48 2012 -0400

    Updated package to version 1.7.2

commit 00b9e51b9991223041f544c81023af2e36bf1477
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Sep 7 13:51:10 2012 -0400

    Added boolean flag to method

commit 3c8c504e50a8a1028115265f399148b3f58e6b2f
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Sep 7 13:26:49 2012 -0400

    Modified method so that it returns a boolean flag instead of throwing an exception

commit c9bd22be6e77f24f1c54770d6fb4e0a7071252f3
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Aug 31 15:36:35 2012 -0400

    Changed calculation of minimum and maximum

commit bffaa47c7f35960b50421d5dbba3e2fa5caab4db
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Aug 31 15:27:37 2012 -0400

    Added method that finds the largest hole in cell by subtracting intensity values and then uses this hole as a seed for adaptive thresholding

commit 21cc7d528e454c2151cf26d33fa5990eb96d62ca
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Aug 31 15:24:03 2012 -0400

    Modified method call to include parameter structure

commit f17a01c0d0dc3bbaa69671deceb42a98a69d4d33
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Fri Aug 31 15:16:38 2012 -0400

    Added routine to determine if any folders are missing and if so, attempt to
    make those folders and approximate the data that belongs in them (i.e. if
    the DNA folder is missing, use the cell or protein folders to find the
    "nuclear hole" and build a mask for the cell

commit 6b59340d70ec0fdeeacd1b6b3a39a9f570e30666
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 16:41:13 2012 -0400

    Updated code to version 1.7.1

commit 5ac5a32a8ba7de677a1ce85492fd35154485b835
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 16:40:51 2012 -0400

    Updated CHANGELOG to reflect changes for version 1.7.1

commit 930110f3c76099492f210e1a76a7b15c2140ed62
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 14:31:57 2012 -0400

    Updated demoinfo to include demos 3D13 and 3D14

commit fa278b4057926d820057d9eed27b0c328bc2b819
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 14:31:22 2012 -0400

    Added syn2projection, a helper method that creates projection from a folder of synthesized images by CellOrganizer. I also included demo3D14, which shows an example using syn2projection

commit b93fdf9fe5c303727055947fbc3b104313843f7c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 14:20:17 2012 -0400

    Added syn2blender, a helper method that makes object files from synthesized images that can be imported in Blender. I also added demo3D13, that shows how to use syn2blender

commit 6e976d3736236a744cc2ae9304207109379028a3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 28 11:23:16 2012 -0400

    Fixed typo in method called that use to call the old methods name. This would produce a warning in older version of Matlab

commit 016a5e45125d78c0ef6d6cdc16a2d51e92c30cb2
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 15:34:19 2012 -0400

    Moved the GUIs to the utilities folder

commit d6afb47795536290b049485cc313f0983147c61b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 15:31:45 2012 -0400

    Reflected changes from renaming of methods

commit 4a40042447d1eb20682cd09bf54ff90c23ded696
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 15:30:55 2012 -0400

    Renamed img2blender to im2blender

commit d109d9ebff82727c6e60c6e04a67e3d3edb65478
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 15:10:27 2012 -0400

    Renamed img2projection to im2projection

commit b956a4e7f795bdd6b8525193e8d5c7381aede20f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 15:06:05 2012 -0400

    Renamed img2plot to syn2surfaceplot

commit 0039d3a1276103edf1a43bc4e3d4dec37398e4b9
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 14:54:16 2012 -0400

    Renamed img2index to ims2index

commit 49bda96198070ffb6ee47ef87121354911dd4f20
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 14:42:00 2012 -0400

    Added README file for demo3D10 that explains how to import the output from this demo to Blender

commit ef4503c247fce798d55f8460da5f4d51efa49a75
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 14:31:24 2012 -0400

    Added PNG file showing the plot from demo3D02

commit 749b68c44aa035af28d4bd52edc1c756d96b94d6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 14:27:34 2012 -0400

    Updated demo3D02

commit b623acf2ffa892456d918abc120dbfc60c84142e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 10 13:41:30 2012 -0400

    Updated version number in setup file

commit 6a98d011f60d5a4b3e510a185882a6a47f5440f1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 8 00:13:11 2012 -0400

    Added all demos, revised all scripts and included all synthesized images

commit 55ecfe93d8409ba5987d26592447690aef54193d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 8 00:06:49 2012 -0400

    Removed old demo folders

commit ffaf7f41fc04cbd15e42df7410fea7612fcc9ba4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 15:57:54 2012 -0400

    Fixed paths in demos

commit 4fc847fd6ce16256ed1eb28ca72d93cc1b45e115
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 15:53:38 2012 -0400

    Removed faulty synthesized images from distribution

commit 984c5885a0bff470416563a3511e728c01a3a943
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 15:51:42 2012 -0400

    Updated CHANGELOG

commit 2094b1295614b0e81051cf846d07d89c8e6ff0cb
Merge: b68bfe0 e1dceea
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 15:28:05 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit b68bfe0370ebd63364aa8448de2ef2a1a6767ade
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 15:27:46 2012 -0400

    Updated images for all 3D synthesis demos

commit e1dceea723c7d5cc9d1c3ba5843f1e3d088ee0fd
Merge: 975f144 9db99d1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 14:59:57 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 975f1444fd016343b5e2ee3c0dff012b046a6160
Merge: d373408 f8c2bd8
Author: Devin Sullivan <devins@cmu.edu>
Date:   Tue Aug 7 11:21:37 2012 -0400

    Optimized code to speed synthesis

commit 9db99d1ef35c6a57513c53b32f0640cab27e9646
Merge: d373408 f8c2bd8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 11:21:37 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit d373408d4816f3aea09e36b239a48ddc3b7f9beb
Author: Devin Sullivan <devins@cmu.edu>
Date:   Tue Aug 7 11:18:11 2012 -0400

    Updated models to reflect changes by previous commit

commit f8c2bd8d038f40b9b2689ea4bcb83b8684c1cb9b
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Tue Aug 7 11:18:11 2012 -0400

    Optimized method

commit 27509cea22ce9760d84d7d373d6ebca3fc1d42f9
Author: Devin Sullivan <devins@cmu.edu>
Date:   Tue Aug 7 10:54:59 2012 -0400

    Changed binning to allow for objects larger than 20 pixels. changed variable names so that the z_x distribution is learned correctly rather than on over written x values.

commit 7f0d42751a8570f117bade27405f1464b9c5b5a6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 07:16:01 2012 -0400

    Removed debugging statement left after testing

commit 92b81a447480b7d5c561cd9dd5788f5e541869d7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Aug 7 00:00:23 2012 -0400

    Updated new models

commit b163f00791510d0c70c3986db27415be5387157c
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 23:52:58 2012 -0400

    Undid some of the previous changes such as binsizes. Go from 0-xobjsize==30 (arbitrarily chosen) and use a max_xbin = 15 (arbitrarily chosen).

commit 97c303371db646de5d735738e2730101057b042b
Merge: 88ffcd6 40560b1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Aug 6 17:59:04 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 88ffcd621ae3ce109ec7a98b449bca178a821199
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 15:44:50 2012 -0400

    Ammended the training of the object size model for the Gaussian model protein pattern

commit 40560b1901b15b7a3c1e8be237be9adbe08c1d92
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 15:44:50 2012 -0400

    Added check that a sampled object is representative of the distribution

commit 88c13f9d29607e4ee79775dfd5822f211608ea01
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 14:18:19 2012 -0400

    Removed "trimmed" method, no longer supported and fixed memory bugs. Moved object sampling inside for loop so
    that the objects don't have to be held in memory before being added. Added check that a sampled object is
    representative of the distribution.

commit 6611a32f9b117015290479780865eaafd6973ddc
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 13:55:08 2012 -0400

    Passed param.nucleus and param.cell from parent call to save memory

commit 81a1ea38ca0ed21589795c41040e1a0a2d43ad7a
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 12:14:40 2012 -0400

    Added param structure to the method, param.imagesize contains the size of the cell image which the objects
    will be added. This is used to make sure we don't waste memory making object images that can't fit in the
    final image.

commit 7fa051c6a835bfc0c867cad36e35bf13dc32b5ed
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 12:10:02 2012 -0400

    Added param structure to the method, param.imagesize contains the size of the cell image which the objects
    will be added.

commit 6cc2febdc2ceb54c5825e2e1c904e726eb16fc8c
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Aug 6 11:51:35 2012 -0400

    Added logical image contrast stretching

commit 490cca6c42953d282bb3731048177f1ba7710d22
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Aug 3 15:15:29 2012 -0400

    Optimized code so that Gaussian objects are generated and added one at a time in order to prevent memory leaks

commit 6f8463bc87d1b6deaace6be7d5e1188471b3d81a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 14:52:57 2012 -0400

    Updated seed in demo3D05 and included the synthesized images

commit 646233bdc301b6a01fee4b666c4b9a1ed4d0a806
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 13:35:14 2012 -0400

    Removed debugging statement left by mistake

commit 40c8f01f15763556b248c5b7203667a98ca74ca7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 13:20:39 2012 -0400

    Included synthesized images for demo3D03

commit 6cb2a908f96ef28de949e8a85261f1c0135cbd41
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 13:19:52 2012 -0400

    Updated seed in demo3D01 and included the synthesized images

commit f16fbc46d460f39a993a2e1fabe75d025a392a8f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 13:15:57 2012 -0400

    Updated random seed in demo3D00

commit 146c5a15c9f4f719a86206d082c96dcb3c23696a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 13:14:05 2012 -0400

    Added images for demo3D00

commit f85b24ffbc6529b55a3537101d5165a02b4ad308
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 08:00:20 2012 -0400

    Update code so that the size of the starting image is greater in size to prevent the synthesis of cell shapes outside of the image

commit 55ff21f1e589396e765e4a62b7171b3d57b26662
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Aug 3 07:57:37 2012 -0400

    Updated new 3D generative models

commit 4394c2b5e2f94ed9b73e99ccf42170dde1e613a4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Aug 2 14:20:14 2012 -0400

    Fixed bug in seg_cell_and_nucleus that was saving the top and bottom slices of the DNA images instead of the cell image

commit 67f1b0d411cacafff345cb09e3fcd6ec91abd0e2
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Aug 2 12:25:27 2012 -0400

    Added masking of protein image using segcell, the preprocessed mask
    calculated when learning the nuclear and cell shape models. This ensures you
    find no objects outside of the segmented cell

commit 77aed881b0889f30694abf8b5b8a7195b479d979
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Aug 2 11:36:11 2012 -0400

    Added debugging statement that prints a message if spline features calculation is not successful

commit c51ce2ba6845e7512cfcc82fbba79dede4f638a8
Merge: b95d2c7 ca1d989
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Aug 2 09:18:56 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit b95d2c71a0cd88f2e4e90b785d5cc818ca98c637
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Aug 2 01:00:53 2012 -0400

    Updated code that learns the Gaussian objects for the protein shape model and made changes to
    the synthesis of nuclear and cell shape as well

commit ca1d9898611ae8cc0286957b3447254ecb2ffa4c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Aug 2 01:00:53 2012 -0400

    Fixed bug where the image directory loop would ignore the first two images

commit 19917c71bddae40c2d1a54a3ee341613a3eabc5e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 1 18:47:47 2012 -0400

    Modified the code so that is saves the bottom slice index and top slice index of the
    original image with respect to segcell.

commit e67185d1fd14c9d969f6ad88ef0ab0b3da8b6cb1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 1 18:23:10 2012 -0400

    Fixed a bug in the code that would insert an artifact to the end of the image that would
    later be considered by the algorithm as an object and affect both the frequency and size
    models

commit 82e8aff70d888e8850de95b20f68e63ebe93e015
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 1 12:42:13 2012 -0400

    Updated 3D mitochondrion model

commit e9b6d82e0bf5f751d8ff0fb6b8c074249b5bebd1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Aug 1 12:41:20 2012 -0400

    Removed copy of ml_loadimage.m

commit 9c7f157055ec6606d6ad20d5c713b989b4883d7d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 31 14:28:58 2012 -0400

    Updated new models: lamp2, nuc and tfr. Moved location of framework model to demo3D11 and removed old definition from SLML

commit f0cd915346e397812cc6a264a1f7505299d0c773
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 31 10:25:20 2012 -0400

    Fixed model.proteinShape.class that was set to lysosome for all patterns

commit db10561cceefca5b4c779f2423c970ccea359a48
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 31 09:16:48 2012 -0400

    Removed removal of temporary folder when synthesizing an image

commit c79939876f82488f5b4e0c0adf413a58518583fe
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 18:10:53 2012 -0400

    Fixed model parameter that describes pattern name. Fixed cytonuclearflag so that it is set to be nuclear when the nucleoli pattern is selected

commit 0c4be4eb0f6e7eab4e0fa2be411f2a67efebd5b5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 17:41:23 2012 -0400

    Modified code that is res files in the temporary folder rather than the folder itself. This way if a user trains a model and synthesizes images in the same script, the temp
    folder remains intact in case it is run in debug mode

commit 9ff8a8008fec1307933a8c3226ac4ec0ea70ebcb
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 17:40:32 2012 -0400

    Fixed support for lognormal sampling

commit 0004ba65a46a93fc0b7cadc84c8a6425e6d51173
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 15:31:58 2012 -0400

    Fixed a bug in the method that would not set theocation of the framework file is the number of input  arguments was not zero

commit d4590adc160b6c035422a663ca36671155979fc7
Merge: fe35ac7 281cee7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 13:47:18 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit fe35ac7cef42031aa2d61da0a3d43a9a4b1e4eca
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 30 13:47:08 2012 -0400

    Optimized code to include a parameter that will filter objects by their size. The default value for this has been set to 10 pixels. The learning of the object size model has also been modified so that it fits to a lognormal distribution rather than an exponential

commit a8e0d25c648b8c6c95fe429c98ed186bbfcd61f5
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Jul 27 19:40:31 2012 -0400

    Included sampling from a lognormal distributions

commit 281cee78ee1a65ee5c02ecd94478936d08c14951
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 19:40:31 2012 -0400

    Updated seed for the random number generator on all demos

commit 7b5f099aac1ed3050c344792980183be3adcf938
Merge: c5a3d93 426973a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 18:04:21 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit c5a3d93b0c8f87d80c59270b6db2c614e78b5c76
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 18:03:30 2012 -0400

    Updated and verified 3D generative models learnt using demo3D12

commit 426973a94eeb4147809b426d628792a71d12e1c8
Merge: 04ff185 4490af6
Author: Yue Yu <yuey1@compute-0-16.local>
Date:   Fri Jul 27 17:36:17 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 04ff185b9e64de7f4348fb37630ccacf614c453b
Author: Yue Yu <yuey1@compute-0-16.local>
Date:   Fri Jul 27 17:36:01 2012 -0400

    Added the new version of slml2model.m to cellorganizer

commit 4490af687d02f0a4ca4d2a2de3d6c2ed42eacb43
Merge: 7d8cb7a 77c01c1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 16:57:53 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 7d8cb7ae66fa534bebaa2e1f7f2d4329771ec97b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 16:57:14 2012 -0400

    Updated the microtubule and centrosome models to include the framework trained using the four protein patterns of the HeLa dataset

commit 77c01c1bce93bf2b9dc2b4959a847ac1ae55f3ae
Merge: 0d02c60 489816e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 16:50:58 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 0d02c600bcaa785feb3dd2887d59a45fbf52d147
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Jul 27 15:35:40 2012 -0400

    Updated CHANGELOG to reflect changes for version 1.7

commit 489816e4a237968102342386ab457083e97ef242
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 15:35:40 2012 -0400

    Update demo3D12 so that it looks for framework.mat in the directories of demo3D12 and demo3D11

commit a55664e36284ee9398ba7fe83a3cd3df3d449034
Merge: 445699b 448dd25
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 15:00:34 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 448dd2516b533adaedc8423518f3e02152007074
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 14:53:32 2012 -0400

    Added demo3D12 that trains a 3D generative model from one of the four protein patterns of the HeLa dataset

commit 17e28b9656d7a7a86220b58d332b545eacef92a5
Merge: 4c51879 f404fd1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 14:10:19 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 4c518797fb28ffc7dcfacb1294dfc11ae66be1c4
Merge: 799c710 fe71d22
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Jul 27 13:24:36 2012 -0400

    Updated all 3D demos and demo information script

commit f404fd19b49c59fdf7bfabf141ce4939c6f96b31
Merge: 799c710 fe71d22
Author: Yue Yu <yuey1@compute-0-16.local>
Date:   Fri Jul 27 13:24:36 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 799c710e0df9f3d6190e68cd8cb32deee9012ed8
Author: Yue Yu <yuey1@compute-0-16.local>
Date:   Fri Jul 27 13:24:23 2012 -0400

    Added new model2slml.m method and use it to generate the xml file

commit 445699b06806f7c0d9f25038b06c491343635d29
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 27 13:11:50 2012 -0400

    Reintroduced try/catch statement on img2model.m

commit fe71d22dcb3a1332aec6a0ed75ec9fd6b38ae972
Merge: db65281 83d8aa3
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Jul 27 12:53:09 2012 -0400

    Updated demo3D08 and demo3D13

commit 83d8aa3d9feb6bfc4dc4511c8f4145aba8bdad77
Author: Yue Yu <yuey1@compute-0-16.local>
Date:   Fri Jul 27 11:17:46 2012 -0400

    Added dimensionality field ti 2D model

commit db65281328a50248c44d402d366686a1c73d1374
Merge: 6ae5a0b 5c497da
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 23:42:38 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 6ae5a0bb5cd3968679ecb451f99a2e97b138480f
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Jul 26 18:07:42 2012 -0400

    Updated method to include priority list

commit 5ae4cff4a2cafd43a172899d9dceaadb44c49aff
Author: Yue Yu <yuey1@lanec1.compbio.cs.cmu.edu>
Date:   Thu Jul 26 18:44:35 2012 -0400

    Fixed three bugs in model training code, now the 2D demos work

commit 5c497dacd29f4206093e1ee17793d6918699a99a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 18:07:42 2012 -0400

    Added helper method that generates an HTML page to view the demo results in a browser

commit b92053024272c3c238f9858003841a75397f84fd
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Jul 26 18:01:39 2012 -0400

    Updated methods to perform bilinear interpolation when resizing images. This update should improve the synthesis of microtubule patterns

commit 7c52a54d0d1be65c03db4dd99e7abb670b398468
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 18:00:09 2012 -0400

    Updated demo information file

commit 0829c66fff573b097fb6310237781060bc04e1da
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 17:52:53 2012 -0400

    Removed debugging statements in method

commit 84aa380ba1006282ceb4731a92ccc2afcccb3eca
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 17:52:16 2012 -0400

    Updated methods that export images to objects that can be imported to blender

commit 2a5904703306dc9af7570ee721d8569e1fef1988
Merge: f8ded42 bb8e3dd
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 17:50:38 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit f8ded42d1f05b0899b51c5d4a867f0a90bf273fe
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Jul 26 15:27:16 2012 -0400

    Added demo3D13 that synthesizes an image that can be imported to Blender

commit bb8e3dd48e186040f00091ed5eb44ff38e76cfea
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 15:27:16 2012 -0400

    Added demo3D11 that trains a generative model of the cell framework using the four
    patterns in the HeLa dataset

commit aa949bbad2c3457789e461071c214d61544ec5fa
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 15:18:45 2012 -0400

    Optimized code so that after segmenting the image, if the number of slices in the
    nuclear image that have fluorescent signal is less than 4, then ignore such
    image by avoiding calculation of both the spline features and the cell codes

commit 14ba4bedfe0c0eb32bdb565b539af0b462c808ac
Merge: c396fd6 c471f0b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 14:55:47 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit c396fd6849b95028f2941960619ba359672927d4
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Jul 26 11:35:04 2012 -0400

    Optimized code for synthesizing microtubule patterns

commit c471f0bc0e6731f828e9ef13c8d485417d0bfb28
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 26 11:35:04 2012 -0400

    Updated demoinfo file to include demo3D10

commit e15f11ed43d15351ee81a88ddbe52cade3be1890
Merge: 09e6ec8 8cf16fc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 16:17:30 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 09e6ec83737e9f01fd1472b5becc8804414f47d6
Merge: fc14266 bb4dcbd
Author: Devin Sullivan <devins@cmu.edu>
Date:   Wed Jul 25 15:03:42 2012 -0400

    Updated slml2img to include a flag to produce output that can be read in Blender

commit 8cf16fcb40228255f4c322f275112b4c6cb1568b
Merge: fc14266 bb4dcbd
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 15:03:42 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit fc142668033cc658b206b2e3e58f9ddcb49471c7
Merge: 9c6a4af 6dfb33e
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Wed Jul 25 14:55:23 2012 -0400

    Updated demo3D00

commit bb4dcbd7e5b7c82c6a2be426351a4c69d5424c8e
Merge: 9c6a4af 6dfb33e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 14:55:23 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 9c6a4afdefeca9498ea9d3897b1e7f2fc3cc3ac0
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Wed Jul 25 14:42:08 2012 -0400

    Implemented new preprocessing scheme to prevent cylindrical shaped nuclei

commit 6dfb33ec400abbef5578e32672d3b1cc754e3a45
Merge: 3499ae6 ecff5f4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 12:57:28 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 3499ae6dc2b6bffbcb5c286e5dd5b2cf04557a9e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 12:56:44 2012 -0400

    Revert "Fixed bug that returned an empty image when protein flag was set to cyt"
    
    This reverts commit a6fd3696a15e1e862ecd28dfde0a8958f5da357a.

commit ecff5f4b3a2e1c9995e3d9c6e5ff73732198de4d
Merge: a6fd369 70cc451
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 25 12:52:00 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer into dev

commit a6fd3696a15e1e862ecd28dfde0a8958f5da357a
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Jul 5 15:12:13 2012 -0400

    Fixed bug that returned an empty image when protein flag was set to cyt

commit 70cc451a107d1dad00c3bf9e82427cfeef84899e
Merge: 7d552f6 0b2a658
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Sun Jul 22 22:35:35 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 7d552f694d6b1260ca39cbbeff671fe82544e000
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Sun Jul 22 21:41:17 2012 -0400

    Added demo3D10 that displays a generated image using img2plot

commit f054b436a244f6d8997ff0d284a13ea8b1cd5360
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Fri Jul 20 16:52:14 2012 -0400

    Added arguments to control colors, viewangles, alpha

commit 0b2a658bdb1de04d09c03e96c3e19b95a43938da
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 16:52:14 2012 -0400

    Updated setup.m to reflect latest version

commit 82d829974d3dc802c64c82364ec41dc9b1de88e3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 16:50:00 2012 -0400

    Updated and verified demo3D09

commit 25bad598b9fbe63839c0872c7e12ece8c1f0cb95
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 15:22:30 2012 -0400

    Updated and verified demo3D08

commit 61275f942ca958d0cef5ba25a506ef3750a101b7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 14:03:55 2012 -0400

    Updated and verified demo3D07

commit b50faea5dc15e40a87c53840711fc55585f89d15
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 12:44:46 2012 -0400

    Updated and verified demo3D06

commit 719a16ab810895375931a74f9f68e6aa2f65272d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 12:43:32 2012 -0400

    Updated and verified demo3D05

commit e6e1d1ec43e1394e52f829b907a3866f59dcfdf8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 10:32:44 2012 -0400

    Updated and verified demo3D04

commit 1fd48d167fce47c021889e2e5e2ad35a84e68dd0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 09:59:29 2012 -0400

    Updated and verified demo3D03

commit 4793fea440752a820200ba0b635f0e03b746bb35
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 09:56:49 2012 -0400

    Updated and verified demo3D02

commit f4de9d7fd92a8ab4d54a345448edc570c0af669e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 09:48:33 2012 -0400

    Updated and verified demo3D01

commit d1652de1f5ccce9fbfd0bc75d15897a135d50493
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Jul 20 09:41:16 2012 -0400

    Updated and verified demo3D00

commit 97d1e960059cdf11ef7df6ea435bcddd0283960b
Merge: 0743aa6 211e7b5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 19 15:46:24 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 211e7b587cc10d46e4105fadf217116aefa8478b
Author: yuey1 <yuey1@andrew.cmu.edu>
Date:   Thu Jul 19 19:42:19 2012 +0000

    Added path change to all demos

commit 0743aa6b199daf810a649c771cc8be77fc672c5e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 19 15:37:50 2012 -0400

    Added wrapper method for img2projection that can make projections from variables and tiff files

commit bd93f06c4f9ce6fbcb26af7b78d74035c6acb24e
Author: yuey1 <yuey1@andrew.cmu.edu>
Date:   Thu Jul 19 17:45:01 2012 +0000

    Fixed a bug for the bottom projection image

commit d875370f662ca0b63230683eb7dbf22a99e12586
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 19 13:03:24 2012 -0400

    Updated CHANGELOG

commit 57d8780f96b762365aadf641d0a58126ad915b48
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 19 13:03:07 2012 -0400

    Added a helper method that makes mean and sum projections of the synthetic images produced by CellOrganizer. The idea behind this method is to provide a quick method for visualizing 3D images

commit c4d862b3f8691312b990931e5fca36697888efbf
Merge: 698b761 3b85e38
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 19 11:50:33 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 698b76118b67e3cfecd025af3e54242676d21342
Merge: bf3b9f2 e53ce3d
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Wed Jul 18 18:22:51 2012 -0400

    Updated demo3D08

commit 3b85e388a4dc6310b7793c57dba7716baf6c0543
Merge: bf3b9f2 e53ce3d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 18 18:22:51 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit bf3b9f2c93ce5ac6e455d4de47bc81046d96afb5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 18 18:19:33 2012 -0400

    Removed saving of temporary file containing the workspace in script

commit e53ce3d0a1cd01bee5b375a925954fe8826f546c
Merge: 68f62ad 728a382
Author: Yue Yu <yuey1@lanec1.compbio.cs.cmu.edu>
Date:   Wed Jul 18 17:03:19 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 68f62ad8764c89022f0111f3eabcfe42db574871
Author: Yue Yu <yuey1@lanec1.compbio.cs.cmu.edu>
Date:   Wed Jul 18 16:44:26 2012 -0400

    Modified the demos, the model name lam.mat is changed to lamp2.mat

commit 728a3821fbfc1edc6348a7d967b5d69520da7b5c
Author: Yue Yu <yuey1@lanec1.compbio.cs.cmu.edu>
Date:   Wed Jul 18 16:44:26 2012 -0400

    Modified the demos, the model name lam.mat is changed to lamp.mat

commit 69cbc14b1a528dab1a891f0c34ffdd037afdee20
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 18 15:42:17 2012 -0400

    Updated generative models that were trained using the performance updates on the 3D active mask segmentation

commit 9e37641df742d63d26704a689590b71e8c7570ea
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jul 18 10:22:49 2012 -0400

    Updated method to ignore objects of size 1

commit 7ce461edb8416b766768dfc2fa03a5290bd18831
Merge: f57e246 830c603
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 10 18:10:14 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit f57e246ff2954d46a1f7b3830447bbd08fcb18a1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 10 18:07:25 2012 -0400

    Removed all tif files generated from demos from git repo. There is no need to include this in the private repo.

commit 830c603b8f5837fa2ba3ee63d37667fce95fd977
Merge: 417caee 57c7d36
Author: Michelle A. Mackie <ma.mackie@gmail.com>
Date:   Tue Jul 10 16:11:56 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 417caeed6da4eb42129ce1c89d73020f3276fbd1
Author: Michelle A. Mackie <ma.mackie@gmail.com>
Date:   Tue Jul 10 16:09:13 2012 -0400

    added img2xml it saves an img as a sparse matrix

commit 57c7d36ad5916ba668aaf02d8945246bf9ab702d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 9 17:24:35 2012 -0400

    Updated code so that when debug flag is set true, it saves the model as a mat file. Fixed bug that replaced the model.id and model.name to the default values. Updated code to include all possible options of the input parameter structure

commit 54f7e096ee865e49210218a39b00ac85694f4ca1
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Mon Jul 9 12:43:46 2012 -0400

    Fixed a bug where it didn't work properly if there were  no 0-value pixels

commit 2f478cc8182aea27b2bd43746c2d0b79fa4223bc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 9 12:25:16 2012 -0400

    Reinstated try/catch statements that will return an empty model if it fails to train one

commit 3d2a27542c81e3b685f171a6c1e5a4262387336f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jul 9 12:23:35 2012 -0400

    Updated code so that when debug flag is set true, it saves the model as a mat file

commit fa6a1a2cfe1896f1eb044d5284dba4c9b946e0bb
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 15:12:13 2012 -0400

    Documented method

commit 73e31e0ec4113968e987630ce924e7ff9d99a63c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 15:10:12 2012 -0400

    Documented method

commit af724380256a44e4cc10eae5a2fb824969f847f4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 15:04:27 2012 -0400

    Documented method

commit d4447185fefc3c8c9d45470a140d6dc31d01e71d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 14:01:06 2012 -0400

    Removed unused file

commit 81bda217f6ca6a7b440c5eacd6f3297907efe842
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 13:54:14 2012 -0400

    Documented method

commit 140817106af6c29676cc209ffbb39583cf98b52d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 13:51:31 2012 -0400

    Documented and optimized method for enhance user experience

commit 3515edfa302fc58e96a8881e422fd04b2bad3958
Merge: 0ad944c b9b96d4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 13:40:07 2012 -0400

    Updated img2blender so that it returns a boolean flag to whether the method was
    successful at saving the file to disk
    
    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer
    
    Conflicts:
    
    	img2blender.m

commit 0ad944c8aa4891ea91621effb7385e9d80756715
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 13:11:36 2012 -0400

    Fixed a bug in the checking of the input arguments that prevented the method from working properly

commit 0f7cef93058a06052a326e5f812dc8f8e4d9baf3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 13:05:34 2012 -0400

    Fixed a bug where the default value of the training flag was not set properly and was throwing and error

commit b9b96d4ced109552783438f931bc57b50a8a1403
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Jul 5 09:32:16 2012 -0400

    Updated img2blender by checking input arguments

commit c9a3c37a818e82b4c155ec65cb5b690a4a281765
Merge: 8cf7e89 4c95df4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 14:49:20 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 4c95df4ec6e9304462e39f86203849b70f025323
Merge: 6cd1542 88d9f36
Author: Michelle A. Mackie <ma.mackie@gmail.com>
Date:   Tue Jul 3 13:49:55 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 6cd1542d8f42e48918b89692dafd568411ec6c51
Author: Michelle A. Mackie <ma.mackie@gmail.com>
Date:   Tue Jul 3 13:44:50 2012 -0400

    Added flag to img2slml that selects what to train

commit 8cf7e897520cc4789e3d75bb3b79f58fc56ca587
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 13:26:49 2012 -0400

    Fixed typo in README file

commit 88d9f36571aa872dfe098c6c99b9def7eee0733d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 13:25:17 2012 -0400

    Removed deprecated/unused methods inherited from the SLML Toolbox and included them as helper methods of isImageFile.m

commit d68eb4606c9074a0ad500e1d03e0ad345b5f380d
Merge: 2d89d09 1db48cc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 13:12:48 2012 -0400

    Merge branch 'master' of git@bitbucket.org:icaoberg/cellorganizer

commit 2d89d0968ae5cd4698af26a18b7078d2161dc39d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 13:12:19 2012 -0400

    Removed deprecated/unused methods inherited from the SLML Toolbox

commit 1db48cc703bcebe52ead7202debcb483c4d4e3b9
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 13:03:41 2012 -0400

    Added CHANGELOG file to keep track of project milestones

commit 6823ed1ce142de60bcd35296524ffcd4a79ded33
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jul 3 12:12:26 2012 -0400

    Added AUTHORS file

commit 28ec8b2e5951d654edf782abd47064ab62b192a9
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Tue Jul 3 12:08:42 2012 -0400

    Optimized active contouring to include a flag so that the user can perform segmentation with the gradient propagation calculated on the whole image, rather than per-slice

commit 5cf225db5db67dd97a2a5a089a149e4b456f1d50
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Jun 25 14:48:01 2012 -0400

    Updated tif2img so that the Matlab array inherits the properties of the tiff, i.e. the bit-depth

commit 81754a91405d516444617553d5238f66b77e773e
Author: Gregory Johnson <gj@andrew.cmu.edu>
Date:   Tue Jun 19 23:49:50 2012 -0400

    Changed ml_findobjs loop to accept images of arbritrary x and y dimension

commit 08098ccc9b4ed18dfdb5b4a8a7e353b1570cebfd
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jun 19 15:47:09 2012 -0400

    Adapted img2blender.m from ml_makeobjfile.m. Added license and documentation. Added checking of input arguments.

commit 3d9635da0a93bb69de15b640d0631f2ec29d6970
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jun 19 15:35:58 2012 -0400

    Added the Wavefront OBJ Toolbox to the utilities folder. This toolbox is neccesary for exporting generated instances to a format the is readable by Blender.

commit b0eff56e8bdc7bbec5f7fb398aa338347b31f0a6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jun 19 15:23:31 2012 -0400

    Removed top header and added a check of the input arguments to img2index.m

commit 89eeab9cb267cd39027fea3899ef7db05c59f38b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jun 19 15:17:44 2012 -0400

    Uncommented the training of the protein frequency model from train_protein_model.m and added documentation to getProteinFrequencyModel.m

commit 511b7897a374a7ee85598c2038b7aefcceaa5b3d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Jun 19 11:50:29 2012 -0400

    Changed index name in the preprocessing for-loops that had the same index name as the main loop

commit b5ad6cd2b56256079996cb98289df1b781d8ff3d
Author: Michelle A. Mackie <ma.mackie@gmail.com>
Date:   Thu Jun 14 13:16:21 2012 -0400

    Removed code for indexed image type 1

commit e4becc344c482f8d8fa0a3c755f21e698dc3ca85
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 15:57:07 2012 -0400

    Removed .gitignore files from repository

commit dd9470f2c141373db40eb336284b122c9f2e059e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 15:52:52 2012 -0400

    Removed python folder

commit 2194f5234c99d45da2240d53db964c2daca925a8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 15:27:15 2012 -0400

    Removed source for python and created a separate repository for it

commit aba2ad10475453e1eb8edb33557324dcaa9c661a
Merge: 3554525 aa61ff3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 13:27:19 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 35545259b29bce8cc67eafd5826215372e82edc7
Merge: 14c6a54 72f1489
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 13:11:30 2012 -0400

    Added demo3D08 that shows the usage of output options

commit aa61ff3d226ee3df98d7fa4634d3b65ad4961224
Merge: 14c6a54 72f1489
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Jun 6 13:11:30 2012 -0400

    Merge branch 'master' of bitbucket.org:icaoberg/cellorganizer

commit 14c6a547cffaa693b120bbdc6e41afe26e2316c6
Author: Michelle Mackie <mmackie@andrew.cmu.edu>
Date:   Wed May 23 14:29:46 2012 -0400

    Added option to slml2img so that users can save the generated instances as indexed images

commit 72f1489d01d174858d2a3ce89e04dc832fcc7373
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed May 23 14:29:46 2012 -0400

    Added empty python folder

commit 5a78c5117499fe015eea1edb0d560a0ec1db4b0b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed May 23 14:18:17 2012 -0400

    Branched matlab and python code

commit 0f1f5313010ad963de53a0ad697527d59e7d436e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 26 18:12:49 2012 -0400

    Updated the 3D LAM model .mat file

commit 8584db21e48099e650780e878c9cbfe0f8a2a005
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Apr 26 17:18:21 2012 -0400

    Fixed the new sampling method to sample positions rather than pixel
    intensities while maintaining efficient sampling

commit c753a5c72589a516e60a104f101d44eb509c9a1d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 26 13:51:56 2012 -0400

    Added new flag to save method to allow saving of large matrices

commit a9b35f90aeab460f7abc69b78343a3faba58572b
Author: Devin Sullivan <devins@cmu.edu>
Date:   Wed Apr 25 16:42:55 2012 -0400

    Changed 'sampled' method to uniformly sample within the vesicle and
    refactored code to optimize running

commit 9d6f802825de913a2f6908e2122f109cb1456712
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 25 14:41:09 2012 -0400

    Added beta version of img2plot

commit c605900e52a27673222a70d4834ffafccde8bda1
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Wed Apr 25 14:40:15 2012 -0400

    Count Gaussian objects found in each major object, not the major objects

commit f0103c377f9f4fdcc3b540f280523f76feedbe91
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Wed Apr 25 14:36:34 2012 -0400

    Correction Gaussian object frequency model

commit 0f9129f5c8fc20421cee6f9b40e65e9dd9502721
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 19 08:47:49 2012 -0400

    Fixed a bug where the protein model arguments where save to another structure

commit 63eb425b7469dbc61aa54a35ce6ee446c61d009f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 19 08:17:21 2012 -0400

    Added frequency model to the 3D generative vesicle model training component

commit b49ea5c5b587efca5d13835d3ab5b55706e4ca04
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 17 14:14:26 2012 -0400

    Added parameter structure to the method and fixed a small bug where the method complained
    because of a missing preallocated beta

commit 00ad118e95d710eb4923466349ea5e1c18e0a8ae
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 17 14:12:04 2012 -0400

    Removed display message from try/catch statement

commit c4cfbc44341c1928cb84e74aed54a097ec888563
Merge: a601335 3268248
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Apr 16 15:12:19 2012 -0400

    Merge branch 'master' of /share/home/murphylab/cellorganizer/source

commit a6013353c4495f8b087308a73237407b9d1e9ab8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Apr 16 15:10:17 2012 -0400

    Updated splash figure to reflect new version

commit 3268248b35dd36c50410e93214497537ddc21c46
Author: Devin Sullivan <devins@cmu.edu>
Date:   Fri Apr 13 10:31:41 2012 -0400

    Fixed typo "tooolbar" to "toolbar" and catch statement from v2.0 to v1.6

commit 2e859f2f35f17f26cdfcb61b3c0124f905daeeff
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 13 06:47:32 2012 -0400

    Optimized centrosomal generation code and reran all 3D demos to reflect the change

commit 6eeb55f7e022c2770f70f74ac22099fed45abebe
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 13 00:33:15 2012 -0400

    Optimized tp_genprotimg.m

commit 9de20b229d50a41a872a8fdc2ad98ff938e54a26
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 13 00:31:30 2012 -0400

    Added bouncing method to microtubule generation

commit 9bdfdfe0cc884790aa5ee6845974e94d8ac8c238
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 13 00:25:07 2012 -0400

    Updated README file for the current version

commit 870b9be7343beaed5d461d163d7287216a81c69b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 13 00:13:38 2012 -0400

    Removed temporary mat files from demo3D01

commit 18a1fa281165af8d8f69ca0da85908e356c1f1b3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 23:57:12 2012 -0400

    Edited setup.m and updated version to 1.0.19

commit 5ee35fac1f5e9373d25a3b8ac474726ba706e4a7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 23:56:09 2012 -0400

    Removed debugging statement that was saving a temporary workspace to disk

commit d8829148789498078d7fb9def58dd651fbb4dbea
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 23:55:33 2012 -0400

    Updated and test 2D and 3D demos

commit 1ae77ec8ff6401f512f22e78b1daa676fb98ba07
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 22:23:17 2012 -0400

    Optimized model generation

commit 5b99b7072e2d792c11e9e4f63c0f922cc969c6b4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 18:27:46 2012 -0400

    Updated centrosomal calls to model2centrosome.m

commit 9f248caaee1fcafe68b0fbc78999f058181386de
Author: Devin Sullivan <devins@cmu.edu>
Date:   Thu Apr 12 18:18:37 2012 -0400

    Optimized centrosomal location generation

commit 784159f1e483b5af3aab951aede0bbd3be2ade84
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 18:16:33 2012 -0400

    Removed demos folder from path

commit 7381d4f8c3aade6d2e5327f76cc36c19deabcfae
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 17:53:45 2012 -0400

    Removed debugging statements and improved logging

commit 5457e402d796a4669bdcdfe665c56261f90f7b32
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 14:43:59 2012 -0400

    Added new 3D models

commit 0192d34a403018fad5bd0c76c2a1b60711368043
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 07:40:32 2012 -0400

    Renamed 2D methods to avoid conflict with 3D methods of the same name

commit 5a9c9cfad4e06a7aa35ea985df7edc0f3f77d5a7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 12 00:33:17 2012 -0400

    Renamed 2D methods to avoid conflict with 3D methods of the same name

commit 15bf5cfc97e2c0ac2b8c796bbb37a87e55c4bebf
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 17:38:54 2012 -0400

    Renamed ml_rdistpca.m to ml_rdistpca2D.m to avoid conflicts with 3D method of the same name

commit b59f2c236d1a9070f086f51426e08d6934559b50
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 17:21:36 2012 -0400

    Renamed ml_estpdf.m to ml_estpdf2D.m to avoid conflict with 3D method of the same name

commit b1b7f3485fdede6349e396dc20a92d0a113972c4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 17:16:15 2012 -0400

    Renamed ml_trainshapemodel.m to ml_trainshapemodel2D.m to avoid conflict with 3D method of the same name

commit 0a5ac66746d1dbaacec1cecc4d6f1efdb5f77ca8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 15:22:00 2012 -0400

    Fixed a bug in synthesizer.m where the code would fail if only one model was used as input

commit dc097cf67bb1065a05bf8c4fb26e1328c60132e0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 13:53:14 2012 -0400

    Added debug flag to demo2D00.m

commit 865d1b4899284ee66e5befdb2c370ababccb5833
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 13:27:34 2012 -0400

    Fixed bug in synthesizer.m that prevented GUI from displaying the images prefix when pushing the "Previous
    Image" button in 2D mode

commit 6761b4ca79767acd89e1974c0ebf3e53a5f970f5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 13:09:18 2012 -0400

    Parameter structure param is set to empty when the number of input arguments is one in method model2img.m
    Added try/catch clause to determine verbose flag. Default is false

commit e0389de47e7bfdf10503a118e52ca4d39bee14d7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 13:01:48 2012 -0400

    Removed default contrast-stretch of image in method tif2img.m

commit a567f88ae581165c46cc2b8476bf78213fe55a98
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 11:49:42 2012 -0400

    Fixed bug on img2slml where the lines of code that saves the images to file were outside of the main loop

commit 704fc1924fd798d6c9d132ac48e692a59938bc0c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 11:48:27 2012 -0400

    Updated demo2D00

commit e6b4df24bdd0f1744ff646ba1fe785d90aae1691
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 11:46:58 2012 -0400

    Update message in setup.m

commit 007f38f8165c04f592f52594995ae8e84e693f05
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 08:39:59 2012 -0400

    Renamed ml_gmmem.m to ml_gmmem2D.m to avoid conflict with 3D method of the same name

commit d3c26a69cc9e11142757f83b7a0d5ab1a4c7ab4b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 08:35:07 2012 -0400

    Renamed ml_objgaussmix.m to ml_objgaussmix2D.m to avoid conflict with the 3D method of the same
    name

commit db15f234c0f80165348173db090b90ba6285fd88
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 08:12:32 2012 -0400

    Renamed ml_imgbgsub.m to ml_imgbgsub2D.m to avoid conflict with 3D method of the same name

commit e1a09062e6c958d479fd8e190b9e58f9b2ab9986
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 07:46:38 2012 -0400

    Added verbose flag to method img2model.m

commit c846702813171f4b42cac208fb2128bbc0808e4b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 00:20:54 2012 -0400

    Added debug flag to parameter structure and set the default value to false in img2slml

commit 463580663ae8d61f88210947d0099eee95eb5f73
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Apr 11 00:01:53 2012 -0400

    Added try/catch statements around every imshow call in ml_parsecell to prevent method from
    failing when isshow flag is true but no windows system is present

commit 5cc81671255b44252ddb25acdc6652a54ac76f22
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 23:58:00 2012 -0400

    Updated version variable to v1.1, the first stable private release

commit 1a62431e50e9479419fb794183c98c9ddcb3d0c6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 23:57:11 2012 -0400

    Added debug flag to parameter structure to img2model so that if the flag is true, then
    the intermediate results folders will not be deleted when training is successful

commit fb90c90d298c0fde05c12c6c754d1f7ce959e505
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 23:51:36 2012 -0400

    Added parameter structure to preprocessing method to hold debug and verbose flags

commit cf877ecda05682b366cdc405452a1de64be5870d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 21:51:52 2012 -0400

    Removed line from img2tif where it saved the image as mat file for debugging purposes

commit 4ec0c4ae11f30250b3eb1a9e38a0c2bdef6919c9
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 21:49:41 2012 -0400

    Fixed a bug in demo2D01.m where the image folders where passed to img2slml incorrectly

commit 4b9d53d0c97227af1094dc94c595bcecb16d977f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 12:39:29 2012 -0400

    Added error stack displays to the methods.

commit 8916778551abf04a29f0782a4bc1298588222bca
Merge: d9d86f7 900a9ed
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 11:08:11 2012 -0400

    Merge branch 'dev'
    
    Conflicts:
    
    	utilities/img2model.m

commit 900a9ed3e66b1678eb960748e5ceab843f2f6cbc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 11:06:25 2012 -0400

    Cleaned and updated model training code by adding comments and removing debbuging variables

commit f6a5c7a9fa35a237088a2770aee93108390f1057
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 11:03:22 2012 -0400

    Updated 2D demos folder

commit 3779332c256f581fbe0eb382f058fe9eefe7df73
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 10 11:01:56 2012 -0400

    Added generated image for demo2D00

commit d9d86f75761d1d9f679d78e83303aac8dd598748
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Mon Apr 9 17:02:59 2012 -0400

    Optimized training and synthesis of 3D frameworks

commit 480c85e900992b5286543aefd5b51b1ee38f9439
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Apr 9 10:52:24 2012 -0400

    * Updated progress information while training a 2D generative model.
    * Modified training code so that it saves intermediate steps when learning the
      Gaussian mixture model

commit 52200833dd18e4c6237490625882e56c205ef5be
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Mon Apr 9 09:38:15 2012 -0400

    Optimized synthesis of 3D images

commit 71bb1d940d8425c3e972b12f5794f704bf65ebd1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Apr 9 09:36:27 2012 -0400

    Updated the 2D demos.

commit 387b73795e9a31a5350b5139fc83783332f42fb7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Apr 9 01:34:01 2012 -0400

    Added call to train_cell_model2 to img2model.m and removed the lines that delete the temporary files
    for debugging purposes

commit 4dc91abf3e37b128cd01535e1d90455260c0d93e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Apr 6 07:22:45 2012 -0400

    Returned to old method to calculating cell codes. Created a parallel method called
    find_cell_codes2 for this purpose

commit 1cc0b26f83cfd540153ed075bae51acecfc5175e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Apr 5 02:29:32 2012 -0400

    Updated code that calculates the cell and nuclear ratios in 3D.

commit 1bfe9e3d2af7557dc6782cb333d660241b2ae3e5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 3 10:45:02 2012 -0400

    Added findn a method that return the coordinates of a 3D array in a similar
    fashion that find does in 2D.

commit 7e1f91f652185ce4fa117eafb1c386a78f4c6702
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 3 09:03:24 2012 -0400

    Optimized the training of the cell shape model.

commit 7047f342b3655d66c30467ce2dd23a41aac7cbe4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Apr 3 08:58:03 2012 -0400

    Added a method to find the closest point coordinate from a point and a surface

commit 6755710c420f23d6fc3b69340155728af3e44c5f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 29 13:39:30 2012 -0400

    Updated .gitignore file on demos folder

commit efb05615ba0b6d21d24f3f9172f48daca5bd9a5f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 29 13:38:51 2012 -0400

    Added demo2D01, a demo for training a 2D generative model of subcellular location

commit b882ba576e691cd9e2c482a6e5c419f625eccfe0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 29 13:25:16 2012 -0400

    Updated model training files so that check the input arguments and return empty models when they fail

commit 6e57c32ef4a8e3596a2ec501aad9c169b60d777c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 29 13:23:32 2012 -0400

    Removed unused temporary matlab file

commit a61a96e89cb1eb16408e6970670a0d1e5a52bf97
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 29 13:23:03 2012 -0400

    Updated .gitignore files so that they do not include the xml file models

commit 828ba8bf45cb04f9a55aef58823b751220c5cf05
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Mar 29 13:21:24 2012 -0400

    Added methods for training the cell shape model that uses center of the nuclear object instead of the center of the nuclear object at each zslice

commit 6b822a1b7f497d3a60280761533865de28320010
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 15:33:16 2012 -0400

    Added verification of input arguments when running in compatibility mode (compatible with SLML Tools).
    Added verification of input arguments when running in default mode (CellOrganizer).

commit 13e98cc6549e76f9bb68a5fe39b0e724a37b3137
Merge: 0ecbf66 de0436f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 11:53:24 2012 -0400

    Merge branch 'dev'

commit de0436f1d4ef1b7928cdd6be174a53678d7a62de
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 11:53:11 2012 -0400

    Added a control structure under which if img2model returns an empty model structure, the method exits

commit d593a3ddf6ee0a0f1a13a5d579931d4150565156
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 11:48:50 2012 -0400

    Added a control structure under which if one or more of the image folders are nonexistent
    or they do not contain images, img2model exits and returns an empty model.

commit 0ecbf6626cf69667e4ff3f710dbe5ea927b5d98f
Merge: 4e72e0b 9f972bd
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 10:50:46 2012 -0400

    Merge branch 'dev'

commit 9f972bd3e8ea7d85539134c8741e6aa842b9f11b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 10:50:00 2012 -0400

    Modified setup.m so that it connects to the CellOrganizer website to download the latestVersion number of CellOrganizer
    It then compares that number with the version number found in setup.m and tells the user whether he should
    upgrade.

commit 4e72e0be8c6a89165043d691109c4dcf8e111ec6
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 28 06:51:04 2012 -0400

    Removed all the debugging statements, and updated the comments and licenses.

commit ffb19772724e4e07d832e5e88089918a2f26c231
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Mar 27 11:40:00 2012 -0400

    Removed top and bottom blank slices from DNA and cell images using bot_slice and top_slice

commit 87ff11cfcb85fa0f45f0785c1391a9f224571f38
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Mar 27 09:47:45 2012 -0400

    Modified the code so that instead of sending a slice of the nucleus when parsing the cell codes, now we use a projection of the nucleus for all slices of the cell

commit 12815dde4d94acfbb5fc9f10d4514b51859ba8c7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 26 15:56:17 2012 -0400

    Check if temporary file exists, if it does it loads and returns preprocessed results

commit b31ad96fd4513549db9c260d7895dad3c774155a
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 26 14:23:00 2012 -0400

    Added image rotation after preprocessing

commit 81f7f6fee53c3ddf98388654a1e873134ded91fc
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 26 14:22:10 2012 -0400

    Removed unused methods

commit 0fa67f7c84b2778eac04a6e5810937c1ddbc7394
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 26 09:08:11 2012 -0400

    Removed blank slices from nuclear image before calculation of the spline features

commit 5431719b424d59049adb0ba7324a3ff14069e74f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 23 16:19:24 2012 -0400

    Updated setup.m so that it checks if there is newer version of CellOrganizer available

commit 6eac398720df3b98ca1d4bfa52e7ba159a6fc1f9
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 23 14:54:53 2012 -0400

    Updated methods to avoid overloading with 3D methods

commit 422510ea6d4137ddf044557c899566b063efc5ba
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 23 14:53:21 2012 -0400

    Renamed ml_traingenmodel to avoid overloading with 3D methods

commit 395dda5c6f838f20d48ccc263a13eeccf839f675
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 23 00:48:35 2012 -0400

    Modified save path directory

commit 7234fd47844769e468d843c9ad32722461ecab0d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 23 00:46:53 2012 -0400

    Fixed bug that was saving the preprocessed images using an incorrect index

commit 3b6cccfd6359ec0ebf94f25da2368df3bc9188ef
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Mar 22 17:14:49 2012 -0400

    Find top and bottom slice separately for cell and nucleus

commit 87492d469a6dd66fed2f3c9f50bb0304f95f89e7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 22 17:08:18 2012 -0400

    Added param.downsample parameter to the two methods that preprocess the images so that users can select a downsample scale

commit 8560680cbaa2e5d64fc28d325f5b6e288cb434cc
Merge: 4b4bb6b f6c4e78
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 22 15:04:40 2012 -0400

    Merge branch 'master' of file:///share/home/murphylab/cellorganizer

commit 4b4bb6b91ebd2bd1c3745d4e187b18c5e038b2e2
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Thu Mar 22 11:07:51 2012 -0400

    Optimized active contour 3D segmentation code

commit 1eefb42940ff2e7877c2b68dad8a05fb0e1b53f8
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 22 10:51:47 2012 -0400

    Changed model.proteinShape.location to model.proteinShape.cytonuclearflag and reflected that change in the models as well as the code

commit f6c4e781de003c4f5b0a293c7ee0777a8c96c720
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Thu Mar 22 10:51:47 2012 -0400

    Changed model.proteinShape.location to model.proteinShape.cytonuclearflag and reflected that change in the models as well as the code

commit 4f1768838e13b1bbeee700dcd7c297048d991664
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Tue Mar 20 12:05:38 2012 -0400

    Replaced micro2psf folder

commit 2d5b6e8c56a9ebc441356b1ba70db31b5c41648b
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Tue Mar 20 11:21:59 2012 -0400

    Optimized the process of generating vesicular model image instances

commit fcb38aeb0459ddf2f2a3d5fbfaabab4ee6f1fb6e
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Tue Mar 20 11:08:28 2012 -0400

    Updated the setup script for loading CellOrganizer into a running Matlab session

commit 17bd3f3d83fb0c9cbc75e4ec5251f5a9356b7442
Author: Devin Sullivan <devins@cmu.edu>
Date:   Tue Mar 20 10:39:27 2012 -0400

    Optimized the process of generating vesicular model image instances

commit 085698b0bc6f1f5b2cd7299835a629999c6788f3
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 19 12:38:37 2012 -0400

    Updated .gitignore files

commit 5990f7b2d7454f09a12cd6455c7af50375410071
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 19 12:36:55 2012 -0400

    Renamed ml_parsecell to ml_parsecell to avoid overloading

commit 9d553f335e944d1bf29f487a0f7b276809d48f96
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 19 12:34:59 2012 -0400

    Fixed a bug where the input arguments of ml_parsecell were incorrect

commit 054fee4b0861caa42545fafd45b8220cb737d70e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 19 11:07:56 2012 -0400

    Changed protein model class from cytoskeletal to microtubule

commit 4a62694dc26b441ad8e021a963268e837ff91406
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Mar 19 10:51:58 2012 -0400

    Updated the microtubule and centrosome models and code

commit 1878f56b2da36fca699d9d54eb0374fecbe6891e
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Mon Mar 19 10:34:25 2012 -0400

    Updated documentation on tp_genprotimage

commit 9ea04547e89893928969cfc0ac6c2643895fec7b
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 19 10:31:38 2012 -0400

    Updated model2img documentation

commit 6e2cc00c018689ab6ed9d14edd543094fbc33a1f
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Mon Mar 19 10:30:09 2012 -0400

    Removed old demos and their synthesized images. Added file demosinfo which displays information about the demos on screen.

commit 9ddaf172f994ec0e851f9d546866281a412cb757
Author: Robert F. Murphy <murphy@cmu.edu>
Date:   Mon Mar 19 10:14:58 2012 -0400

    Updated demos folder

commit fd9cd8d842966b2f0292e6166ede4c22f8c5d1a7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Sat Mar 17 05:52:43 2012 -0400

    Updated the code for generating vesicular samples as well the code for saving the images to file

commit 669dd6e10b035e28cf3e83524f7385d03207d7c0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Sat Mar 17 05:41:59 2012 -0400

    Updated demos and synthesized images

commit 6d5b76b3de3ebcb6c1070feee6b54a144b8854c7
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 15:04:44 2012 -0400

    Updated nucleolus 3D model cytoNuclearFlag

commit 7d9eb08c0ee30597612b0a5617856f201b0dbdc4
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 15:01:07 2012 -0400

    Updated demos

commit 73469423bf038e79a94531669dda2e83f3552d61
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 15:00:22 2012 -0400

    Added .gitignore files on demos folder

commit d10a81b552a1cd2a9ef20062c7f08d797c32fdf5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 14:59:05 2012 -0400

    Updated callbacks on trainer

commit 025861cdc15bd44d6d2fd5138ca65880950fb367
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 14:58:23 2012 -0400

    Removed all old demo files and demo3D12. Removed old Active 3D Contour segmentation code

commit b0ce5c9ab34d8f4813dc779ffc3bd7cb4ab04eba
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 16 12:09:59 2012 -0400

    Added new preprocessing method based on Aabid Shariff's code for training microtubule patterns

commit 986082aacc03942682b72ed16d17ba14acc5ad50
Author: Devin Sullivan <devins@cmu.edu>
Date:   Wed Mar 14 14:44:11 2012 -0400

    Fixed sampling method and added sampling density argument

commit d2db14c78a2ce4f7ffbc62454e3ddd130ec39afa
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 14 14:04:25 2012 -0400

    Added and edited demo3D12 which synthesizes 3 images using the nucleolus model with location parameters
    {'cyto', 'nucleus', 'all'}

commit be439ecd020b1cff75021727e457295b8bb40d3f
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 14 13:32:06 2012 -0400

    Updated log file report of parsed files to report a percentage on screen

commit 4f8449541f188c74a3050022860f2ef3c46088ae
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 14 13:10:43 2012 -0400

    Made it sure .git folder is not added to Matlab path

commit 6772e7c6b89919343268575dd101dc37c5691547
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Wed Mar 14 12:47:44 2012 -0400

    Added protein.location parameter to slml2img

commit d1cd82e5e756599d9e090eee874650b5936cc31e
Author: Devin Sullivan <devins@cmu.edu>
Date:   Wed Mar 14 10:44:01 2012 -0400

    Added downsampling and upsampling to MT_synth

commit 92a693404148525ffd732e172b473f8bf93c5519
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 15:48:18 2012 -0400

    Added sampling density parameter to gauss_sampler

commit ddf5eb05ce96898db4ca4cad2df546df1a7f638d
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 15:44:50 2012 -0400

    Added header and documentation to gauss_sampler

commit fcf07bef35b6d0d4ab2920f0ab12d563813b0c62
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 09:17:13 2012 -0400

    Added new header documentation and support for the new method as well as
    providing backward compatibility for SLML Toolbox

commit 15f8a0cf639d8f702ece656b1bd240b5b2c54609
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 09:16:19 2012 -0400

    Updated the progress report so that it overwrites the previous report with blank spaces
    before replacing it with the new report. This is done because sometimes the next report
    is smaller than the previous and the new string gets mixed with the old.

commit 36c3f470aa61ef3976b4eaf6e9c8ff9be8dcec34
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 08:20:05 2012 -0400

    Modified sampling text on GUI. Changed it to 'Sampling density'

commit b14073f938b4fb11ac1477f85f37503eab49d417
Author: Devin Sullivan <devins@cmu.edu>
Date:   Mon Mar 12 02:14:12 2012 -0400

    Modified downsampling/upsampling code on nuclear and cell shape model instance on MT_synth

commit 12d9daa2130481ecb3bada12f6b1d4e72ba65a2e
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 02:12:23 2012 -0400

    Update documentation and cooments on demo2D00

commit 9f8a5eb4aae1a0ad24d411d6a24288b1ddf9319c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Mon Mar 12 02:11:55 2012 -0400

    Updated the documentation on img2slml

commit 31a46a6849623a50b5260131d9276642fb75ff44
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 16:26:32 2012 -0500

    Removed print of progress bar from log file on slml2img

commit e2c50aaa09a2900bf49f5bbf98f7598e703e0ec1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 14:22:38 2012 -0500

    Added license, updated opening and closing functions and removed support for gallery on toolbar

commit ac08e747d7b4839c645fb37493241e709dc65ea0
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 13:38:12 2012 -0500

    Added license to startup

commit a76450f8adc0358ea306f333b7a324f51cb9e6e1
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 13:36:28 2012 -0500

    Updated license and changed SLML Toolbox errors to match CellOrganizer on setup

commit 5ba7525f5ba43b98c4d15a1fbcb82fa2dae00e53
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 13:29:55 2012 -0500

    Added license, documentation and updated the opening and closing functions on synthesizer

commit b451a4b31e07ace1d635f927c5abb042cd4d2134
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 13:18:28 2012 -0500

    Added license, documentation and updated the opening and closing function.

commit 15adea117c65686ed72dddaf5bfc66389312b914
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 03:05:44 2012 -0500

    Changed report of synthesized objects in tp_gengaussobjs

commit d2a31a14b57bb1216b2605aba64e5b4c3e9cca52
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 02:46:13 2012 -0500

    Commented out sampling density, changed disp to fprintf and improved logs in model2img. Removed a new line feed from a fprintf from slml2img.

commit 64b8715e5edacdd7c5f9dc1fc55dcaef8764304c
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 02:05:20 2012 -0500

    Changed disp to fprintf and improved logs in slml2img

commit ff0c7cb7a8811d4e355a36cff50765aa36bcf5c5
Author: Ivan E. Cao-Berg <icaoberg@cmu.edu>
Date:   Fri Mar 9 00:51:16 2012 -0500

    Initial commit
