Diffusion BIOP Run Macro (master) History

History
mastercd8abf46137d447583b8dcf…

Feb 22 2011

Coloc 2: Add PDF printing button to SingleWindowDisplay
6f4f4ebcd8bc
·Tom Kazimiers on Feb 22 2011, 10:50.
Coloc 2: Make MetaCursor more robust
81aa43b1860b
·Tom Kazimiers on Feb 22 2011, 10:49.

Feb 20 2011

Coloc 2: Track all open SingleWindowDisplays with the help of a static list
2f2b99ce0cfb
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Force line width of regression to one
969e0416ee0e
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Reorder readout of GUI and add PSF and nr. of randomisations inputs
332c163846e0
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add two more irregular ROI test cases, similar to regular ones
8ef05d5d880f
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a black/white rectangular mask creation method for use with tests
aa4e589aeee0
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make MaskCursor able to repeat lower dimensional masks
e1db470b2b6b
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
b8806b8cb5a2
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the MaskedImage reuse offset and size of RoiImage
c525e1e78cbc
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add two more regular ROI test cases
facfb0f10202
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Fix existing regular ROI test to use "more realistic" ROIs
76a5696381bc
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Fix small bug in RoiImage and rename members for better readability
520128a17016
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make Gaussian smoothing optional for simple noise method
a9d4c4f02da9
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add simpler access method for Gaussian smoothing for use in tests
2d0b8b9d5deb
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add helper method for combining imglib images
ad37ffe68378
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a Costes unit test case, similar to one in Costes' paper
8a6cf2bc76ef
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add two helper methods to make images binary
33070f98a04b
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
bf3a52efaa9f
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Set Costes' default PSF size to 3 (was 1!)
94624b47ae5e
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Don't let all Pearson's calculation fail if threshold fits not all
776a4153e30d
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add Perlin noise generation for test images
23172aa1b6cb
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add unit test for statistics class
0ecf1fd154df
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Put statistics calculation in Constes' into own class
d04944bf0d2e
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make Costes more robust, be more fault tolerant
83a53827dd7d
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make Pearsons Algorithm a bit more consistent, use error values
dd016cccfbe8
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: State number of iterations done on numerical error in Pearsons
4689ee59c159
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let Fiji handle the MissingPreconditionExceptions
895181d6d658
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make irregular ROI/mask test case simpler
534eba45bd3b
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make stick noise generation accassible without auto smoothing
4613ac7f5684
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Fix use of ImageJ in noise image generation for test images
941569d98760
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add one more Pearsons test with random noise data
b9959f588de7
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a basic Costes significance test case
bb1a3a9a4d0e
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add missind comment to mean based noise image generation method
b0dc7d814a40
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add another random image generation method, it spreads random sticks
ab09cb4aeeff
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make the data generated by Costes (e.g. P-Valu) accessible through…
b12eb8e55259
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: new test image creation method for images with a mean and a spread of…
080904f047f6
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: make testImage creation methods public
9c66d2959aa6
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: add test for if only 1 image is open
2af57cb09b8a
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: made a gaussian smooth method in the testImageAcessor class
84578fb00580
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: remove override annotations for eclipse on mac can do the junit tests
6feff976b720
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make PDF count for multi rois start start with one
3460046cc363
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
30a52606f3a3
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add basic irregular ROI/mask test. Mask self with self and inverted
c92210835267
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add helper methods for tests to invert imglib images
f078dee6de2a
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Allow masks to be specified as separate images
f1df82a5f470
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Select the correct Fiji image when importing masks
747233aa0579
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add own little bounding box class to represent multi-dim BBs
6bc0b7742897
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add lost functionality to colocalise images withoul ROI/mask
888ae16cdc25
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Move our imglib modifications to the right namespace
08ad99cbd48d
·Daniel James White / Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add "_mask_<staticCounter>" to PDF file names if mask/ROI in use
920cd0b527f3
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the DataContainer know whether there is a regular ROI in use
631f286a68bb
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Remove unnecessary if and complain about missing separte image masks
a23eea34ba5a
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make Image data handling in EasyDisplay more type safe
c6ec56d45813
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Do some generics argument adding, clean up, code police
e159abb4e0ae
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add basic multi ROI support
7e5d4bf7374f
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Tests: Change sample image type to UnsignedByteType
83adab3c1b62
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add simple test case for regular ROIs
fbc942924a9a
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Change package declaration of ImageStatistics to reflect folders
1e8cf3a2803d
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: be more friendly at RoiImage initialisation
dd0d04893660
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Move image statistics class to better fitting namespace
83ec3afc187f
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Fix typo in gadgets folder
38731e4045cc
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: For now disable the display of the shuffled date from Costes
03e4c0b1e934
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Allow masking in Costes stasitical significance test
c10ccc3e62c6
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Remember a masks bounding box clipped version
2fbc9492f8a0
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the MaskImage use the LocalizableByDimCursor from RoiImage
71640c6be85b
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Reuse LocalizablePlaneCursor from super cusors in Roi/Mask
e2f2392158a6
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: In RoiImage return 1 if dimension request is out of range
8fda1427eb47
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Remove override for factory and image creation methods in RoiImage
d43de45fd202
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: In Costes, create OutOfBounds ROICursors through image types
421098ef20eb
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
1ff364e98842
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Require the offset and the size of a masks bounding box
f8e95e85c0d6
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Encapsulate irregular IJ mask preparation in own method
c0144f22f82e
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the mask cursor repeat the mask if it went through it
ab8360b65c59
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add ROI/mask image (if present) to result set
744469522413
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let RoiImage use RoiShiftingLocalizableCursor
af91b413aa77
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Clone ROI information in RoiImage, data must be no reference here
d841fe090453
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a LocalizableByDim cursor that shifts ROI cursor reguests
75c78997642c
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a RoiImageFactory
745130554bb3
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add MaskedImageFactory to create new images based on MaskedImages
498a29defbb5
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add some image properties to the RoiImage
817874919522
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make MaskCursor hierarchy deal with mask image insdead mask image
03a1a9295789
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make members of ConstraintCursor protected
ebd93d98a514
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the ROI cursors in Costes' be implicitely by the image type
941711f0d5e7
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Split MaskCursor in MaskCursor and MaskLocalizableCursor
7717a9c26899
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
612f7b21fbe4
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Remve not needed roi usage indicator variable
1668807d4d09
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add ROI/Mask selection to GUI
2b8f0d4e5b8f
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style changes
a0cca6fd0d74
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Let the plugin allow ROIs again, now arbitrary shaped
7d3b617723e4
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: The DataContainer can now create MaskedImages if required
7e5fe0b13de6
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add MaskedImage
305a24545c73
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make MaskCursor a LocalizableCursor and change the typing
0b0c663d5693
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add ForwardMode setter to ConstraintCursor
27c7ac4ca4ae
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Make the MetaCursor implement the Cursor interface.
25214f0ca681
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add ConstraintCursor to make TwinValueRangeCursor logic reusable
4d2b7fa5ba7e
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add basic mask cursor implementation
ba4af822eb98
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Style and Comment changes for TwinValueRangeCursor
5cc5097d828a
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: Add a missing class to the imglib extensions: MetaCursor
3f8591265459
·Tom Kazimiers on Feb 20 2011, 22:33.
Coloc 2: In PDF output add no horizontal rule after last image
be16034dd9a0
·Tom Kazimiers on Feb 20 2011, 22:33.

Historymastercd8abf46137d447583b8dcf…

Feb 22 2011

Feb 20 2011

History
mastercd8abf46137d447583b8dcf…