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BatchVerMo #20

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Commits on Jul 5, 2017

  1. new input “manual”

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    shijiegu committed Jul 5, 2017
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Commits on Jul 6, 2017

  1. use central A to merge

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  2. gt not lt…stupid

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  3. chucked version faster

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  4. New Merging strategy: quit using original functions from C++

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  5. Splitting added, viewTraces added. More robust input/output parser.

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  6. changing the trunked version

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  7. stupid mistake

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  8. something about std

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  9. some ind error. now fixed.

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Commits on Jul 7, 2017

  1. debugging display added :(

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  2. more display

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  3. added isempty(…)

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  4. shoji’s own merging function’s debug

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  5. sequence change

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  6. mergeAC adding debugging information newIDs

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  7. some unnecessary changes revert

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  8. having new changes in upstream

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  9. debugging MergeAC

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  10. cat(dim,….)

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  11. min_pixel included as a user defined parameter in BatchVer

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  12. debugging the problematic peeling off process. chasing ci to ci_raw

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  13. c_raw seems to be fine!

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Commits on Jul 8, 2017

  1. higher PNR; median to mean

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  2. (1) Make sure c’s are the same. (2) Only have neurons that are merged.

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  3. typo

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  4. typo

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  5. Full version, using bout files.

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Commits on Jul 9, 2017

  1. after merging, some files may have zero neurons. This update take int… 

    …o account of this.
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  2. display

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  3. many check point for empty results added!

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  4. more check points

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  5. bout1 and bout115 has different character number!!!

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  6. selectedTraces added here

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Commits on Jul 10, 2017

  1. small changes but might be important!

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  2. before pull request

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    shijiegu committed Jul 10, 2017
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Commits on Jul 12, 2017

  1. not allowing massive mode to deconvolve

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    shijiegu committed Jul 12, 2017
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  2. allow deletion in spatial

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    shijiegu committed Jul 12, 2017
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Commits on Jul 13, 2017

  1. for deconvolving

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    shijiegu committed Jul 13, 2017
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Commits on Jul 18, 2017

  1. add Afinal saving as well as ColoredA for each batch for moBatchVer

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    shijiegu committed Jul 18, 2017
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Commits on Jul 19, 2017

  1. Afinal, not Amask

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    shijiegu committed Jul 19, 2017
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  2. “normcorre” forBatch underdevelopment

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    shijiegu committed Jul 19, 2017
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Commits on Jul 22, 2017

  1. moBatchVer cluster part starting!

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    shijiegu committed Jul 22, 2017
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Commits on Jul 23, 2017

  1. motion correction included. Basic version cluster part changed.

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    shijiegu committed Jul 23, 2017
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  2. Changed ColorAllNeurons so it doesn't autosave

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Commits on Jul 25, 2017

  1. colorallneurons pushed by git

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    shijiegu committed Jul 25, 2017
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  2. Merge branch 'BatchVer' of ssh://bitbucket.org/feelab/cnmf_e into Bat… 

    …chVer

# Conflicts:
#	BatchVer/ColorAllNeurons.m
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Commits on Jul 26, 2017

  1. BatchVerMotion Cluster1 is shortened and these cut are put in Cluster2

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  2. renaming cluster part1

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    shijiegu committed Jul 26, 2017
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  3. commit changes before renaming

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    shijiegu committed Jul 26, 2017
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  4. renaming cluster part2

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Commits on Jul 27, 2017

  1. BatchVerMo

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  2. demo update

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    shijiegu committed Jul 27, 2017
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  3. BatchVerBasic

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    shijiegu committed Jul 27, 2017
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  4. add ending note

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    shijiegu committed Jul 27, 2017
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  5. outputdirDetails

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    shijiegu committed Jul 27, 2017
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  6. dir issues

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  7. cd

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    shijiegu committed Jul 27, 2017
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  8. BatchVerMotionSection

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    shijiegu committed Jul 27, 2017
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  9. new version

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    shijiegu committed Jul 27, 2017
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  10. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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  11. one file is small the other is bigger

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Commits on Jul 28, 2017

  1. some changes before

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  2. some for BatchVerMo

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  3. MergeACforMo will only calculate index but do not the actual merge. T… 

    …he actual merge will be done by reducing A.
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  4. Some update for Merging in BatchVerMo. Office is too noisy Going to L… 

    …aw School Library for the rest.
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  5. Merge for cnmfeMoBatchVer

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Commits on Jul 29, 2017

  1. NewVersion of Motion Correction- 1) limited update 2) Nuerons out of … 

    …FOV deleted.
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  2. wrong name specification

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  3. folder problem again

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  4. new version format change

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  5. Structure concat change

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  6. Some structures are concated in the other direction

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  7. M was saved as M_final not M in MotionCorrection Section...

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Commits on Jul 30, 2017

  1. Merging debug1

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  2. Trunked Version for testing stage

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  3. typo

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  4. some index stupid typo

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Commits on Jul 31, 2017

  1. mergeAC typo. some new normcorre_BatchVer debug

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  2. Using consecutive day’s relative shifts to infer all shifts among days

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  3. reducing the memory use

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  4. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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Commits on Aug 1, 2017

  1. Looks like in our design, only keeping neurons that are found in at l… 

    …east 2 files/days will work.
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  2. before my computer goes to repair. Here is new inter-day registration

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Commits on Aug 2, 2017

  1. This commit is the debugged-version of updating pics to register rath… 

    …er than updating template or simple shift matrix addition/subtraction.
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  2. This version uses overlapping information between days to align.

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Commits on Aug 3, 2017

  1. motionGUI

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Commits on Aug 4, 2017

  1. magnifying, indexing, automatic aligning one neuron pair

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Commits on Aug 5, 2017

  1. Making GUI nicer, ready to move neurons tmr

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Commits on Aug 6, 2017

  1. added text in GUI, fixing some bugs in reverse

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  2. neuron recognition in process

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Commits on Aug 7, 2017

  1. Basic GUI complete

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  2. use the middle M

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Commits on Aug 8, 2017

  1. ...the missing one

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  2. Trunked has some changes important changes

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  3. MotionBasicDone

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Commits on Aug 9, 2017

  1. Merge commit '9ecacc94592e1bd0d7557f01e171a81fcb78023e' into BatchVerMo 

    # Conflicts:
#	ca_source_extraction/@Sources2D/Sources2D.m
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  2. merging BatchVer and MoBatchVer

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Commits on Aug 10, 2017

  1. Merging all motion correction scripts into GUI

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  2. This GUI version includes NormCorr "auto tune", grid drawing, and par… 

    …ameter input.
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Commits on Aug 11, 2017

  1. missing d1 and d2

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  2. some missing variables

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  3. some missing variables

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  4. Whatever I can do on Motion Correction

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  5. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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Commits on Aug 15, 2017

  1. Making raw video's background subtracted video for each day.

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  2. Making movies, some changes on my mac

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  3. maybe the dot

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  4. checking

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  5. making movies name diff

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  6. double

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  7. adding raw data in File

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  8. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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  9. Making videos; adding raw data in save.

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  10. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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Commits on Aug 16, 2017

  1. some bugs in making movies, also making raw data movies for reference.

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  2. Size change of GUI

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  3. annoying video making

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  4. stupid typo

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  5. typo

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  6. Using C_raw for merging neurons

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  7. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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  8. typo in comments

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  9. I forgot some changes in the format

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  10. Added try and catch for movie making

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  11. shortened version

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  12. Fixing deconvolutuion

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  13. Merging

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  14. making better videos and deconvolution fix

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  15. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo

# Conflicts:
#	BatchVerMO/MakingVideos.m
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  16. Last debuging before running

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  17. Use updated A for merging

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  18. video bugs 3

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  19. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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Commits on Aug 17, 2017

  1. Important typo

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  2. changing the way to extract c from a. Now back to PC’s original method.

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  3. typo

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  4. index issue/typo

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  5. corr image making

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  6. function’s missing input

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  7. some small bugs

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  8. size and nan

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  9. use weighted version

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  10. something not important now

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  11. merging

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Commits on Aug 18, 2017

  1. Filtering out some neurons

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  2. some index typo

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  3. updating some changes made in Part1 in Part2.

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  4. day typo

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  5. added raw traces

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  6. typo

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Commits on Aug 19, 2017

  1. part2

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  2. merging branches

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Commits on Aug 20, 2017

  1. get back to normal

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  2. temp to C

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Commits on Aug 21, 2017

  1. some changes

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  2. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  3. debugging

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  4. merge branches

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  5. some small changes

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  6. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo

# Conflicts:
#	BatchVerMO/DEMOforMoBatchVer.m
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  7. more efficient. 

    adding neuron deletion in GUI for manual inspection.
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  8. merging branches

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  9. more changes regarding to variables.

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  10. Adding cnacel deletion option

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  11. more debugging information included

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  12. missing part

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Commits on Aug 22, 2017

  1. small trick

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  2. some mistakes I made in Columbia

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  3. some tricks for global variables Hope it will work

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Commits on Aug 23, 2017

  1. weird matlab parfor

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  2. parfor nightmare

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  3. smaller data set

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  4. adding display line

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  5. debug

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  6. try object copy rather than equation

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Commits on Aug 24, 2017

  1. final changes

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  2. final code cleaning/commenting---1

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  3. more cleaning

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  4. cleaner DEMO!

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  5. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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Commits on Aug 25, 2017

  1. DEMO more concise

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  2. Merge commit '098c6b3a408fc363d907322c1d61a1bcedbafb15' into BatchVerMo 

    # Conflicts:
#	ca_source_extraction/@Sources2D/updateSpatial_endoscope.m
#	ca_source_extraction/@Sources2D/updateTemporal_endoscope.m
#	ca_source_extraction/endoscope/extract_ac.m
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  3. cleaning code

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  4. merging branches

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  5. changes some video making

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  6. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  7. A2C2A

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  8. raming A2C2A to A2C

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  9. some cleaning

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Commits on Aug 26, 2017

  1. missing line

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  2. a small bug

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  3. merging branches

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    shijiegu committed Aug 26, 2017
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  4. more cleaning

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  5. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  6. cleaning the “filelist” and “sample list”

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Commits on Aug 27, 2017

  1. using previous version

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  2. back to before

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Commits on Aug 28, 2017

  1. more cleaning

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  2. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  3. more cleaning

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  4. just to make life easier

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  5. move some of the contents of the script to the shell script.

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  6. missing changes

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Commits on Aug 29, 2017

  1. trunked

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  2. new DEMO

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  3. move it here

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Commits on Aug 30, 2017

  1. final cleaning

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  2. small changes

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  3. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  4. …

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  5. some older version cleaning

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  6. merging branches

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Commits on Sep 2, 2017

  1. something I messed up during the last cleaning...

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Commits on Sep 3, 2017

  1. new version did not update in the outside

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  2. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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  3. … folder problems…

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Commits on Oct 2, 2017

  1. Add a function for getting giff from M3 in NicerA

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  2. 1) Only use neurons that appear in each day. 

    2) ColorAllNeurons plus PNR in the picture name.
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  3. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
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Commits on Oct 16, 2017

  1. Some changes in saving format

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  2. part traces returns deconv spike times

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    shijiegu committed Oct 16, 2017
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  3. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
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    shijiegu committed Oct 16, 2017
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Commits on Oct 28, 2017

  1. minor changes

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    shijiegu committed Oct 28, 2017
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  2. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo

# Conflicts:
#	BatchVerMO/DEMOforMoBatchVer.m
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    shijiegu committed Oct 28, 2017
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  3. part traces, don't divide deconvolved S by pnr

    @shijiegu
    shijiegu committed Oct 28, 2017
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Commits on Oct 30, 2017

  1. including spike

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    shijiegu committed Oct 30, 2017
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Commits on Oct 31, 2017

  1. newer version

    @shijiegu
    shijiegu committed Oct 31, 2017
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  2. ….matlab version issue

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    shijiegu committed Oct 31, 2017
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Commits on Nov 1, 2017

  1. some minor changes!

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    shijiegu committed Nov 1, 2017
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  2. Merge branch 'BatchVerMo' of https://bitbucket.org/feelab/cnmf_e into… 

    … BatchVerMo
    @shijiegu
    shijiegu committed Nov 1, 2017
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  3. some version issue

    @shijiegu
    shijiegu committed Nov 1, 2017
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  4. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo
    @shijiegu
    shijiegu committed Nov 1, 2017
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Commits on Nov 8, 2017

  1. pic name change

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    shijiegu committed Nov 8, 2017
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Commits on Nov 26, 2017

  1. sometimes the noise estimator leads to failure. This should be caught… 

    … by “try/catch”, using the alternative method.
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    shijiegu committed Nov 26, 2017
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Commits on Nov 27, 2017

  1. for 6938

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    shijiegu committed Nov 27, 2017
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  2. trunked for the long 6938 dataset

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    shijiegu committed Nov 27, 2017
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Commits on Dec 3, 2017

  1. For the bug in noise estimation. estimate_baseline_noise sometimes cr… 

    …eates singular matrix. In this case, use GetSn for safer result. Warning is transformed to error to use try/catch to catch it. Ref: http://undocumentedmatlab.com/blog/trapping-warnings-efficiently
    @shijiegu
    shijiegu committed Dec 3, 2017
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  2. typo

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    shijiegu committed Dec 3, 2017
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Commits on Dec 5, 2017

  1. Some files have inherent defects in them, estimate_baseline_noise see… 

    …ms to be a very good finder for this. Thus I catch the error and return a warning that the file has defects, double-check.
    @shijiegu
    shijiegu committed Dec 5, 2017
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  2. return, not break

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    shijiegu committed Dec 5, 2017
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Commits on Dec 6, 2017

  1. Corrupted files are considered to have frame-drop. Noise estimation i… 

    …s changed to not to drop file, but just to use a second way.
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    shijiegu committed Dec 6, 2017
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Commits on Dec 9, 2017

  1. I do not know matlab changed this.

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    shijiegu committed Dec 9, 2017
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Commits on Dec 26, 2017

  1. Merge commit '088afc143f84d384c38c50e7c3cda6f040e5f57a' into BatchVerMo 

    # Conflicts:
#	.gitignore
#	ca_source_extraction/@Sources2D/Sources2D.m
#	ca_source_extraction/@Sources2D/quickMerge.m
#	ca_source_extraction/@Sources2D/updateTemporal_endoscope.m
#	cnmfe_scripts/cnmfe_quick_merge.m
#	deconvolveCa/deconvolveCa.m
    @shijiegu
    shijiegu committed Dec 26, 2017
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Commits on Jan 11, 2018

  1. Shijie wrote this on Emily's computer: greedyROI initiation now inclu… 

    …des automated min_pnr detection. It needs threshold_by_diff to work. In writing, the testbed is SomeAutoamationProcess.m.
    @emackev
    emackev committed Jan 11, 2018
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  2. merging new changes from PC

    @emackev
    emackev committed Jan 11, 2018
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Commits on Jan 15, 2018

  1. Shijie: using PC's code

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    emackev committed Jan 15, 2018
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Commits on Jan 20, 2018

  1. Adding Transformation as the output.

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    shijiegu committed Jan 20, 2018
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  2. empty nam

    @shijiegu
    shijiegu committed Jan 20, 2018
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  3. Merge branch 'BatchVerMo' of ssh://bitbucket.org/feelab/cnmf_e into B… 

    …atchVerMo

# Conflicts:
#	demos/demo_batch_1p.m
    @shijiegu
    shijiegu committed Jan 20, 2018
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