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Recons dti workflow #1121

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wants to merge 315 commits into from
Closed

Recons dti workflow #1121

wants to merge 315 commits into from
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Commits on Aug 30, 2016

  1. Add single line creation and tests

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  2. Add logging consistency test

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  3. Removed explicit path in test

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  4. Add quick load for images

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  5. Simple nifti save + test

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  6. WIP introspective IOIterator creator

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  7. made two lines one line

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  8. Slight fixes to io_iterator, pipeline wip

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  9. Implemented io_iterator in all workflows except pipeline

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  10. wip on output paths generation

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  11. NF: save/load peaks as NPZ

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  12. NF: new CSD workflow that generates peaks

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  13. NF: new deterministic tracking flow. Hopefully simpler than before. T… 

    …he input now is PeaksAndMetrics!
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  14. RF: renamed bin file for deterministic tracking

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  15. BF: wrong flow corrected in dipy_reconst_csd

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  16. BF: had to remove some inputs

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  17. BF: I had to save the vertices of the sphere from peaks not the entir… 

    …e Sphere object. You can only save arrays in .npz files. I think.
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  18. Continue working on output gen

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  19. io_iterator now creates directories

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  20. Reworked io_iterator, tests are still wip

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  21. minor updates in flows

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  22. Fixed io_iterator_ calls in flows

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  23. RF: cleaning up older tracking code

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  24. NF: added workflow for masking images

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  25. Updated tracking with an extra input of a seed mask

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  26. BF: corrected path in of seeding_mask

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  27. Corrected typos

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  28. Delete old and unmaintained binary files

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  29. Implemented workflow as objects

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  30. Fixed scripts

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  31. Fixed scripts again

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  32. Added force mecanic, finished implementing new pipeline

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  33. Completed new pipeline

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  34. test for install and quick pipeline

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  35. Moved flow_runner in dipy.workflow, makes more sense.

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  36. Fixed streamline save problem

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  37. Added skip mechanic, fancied the pipeline directories creation.

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  38. Fixed TDI out_directory in the pipeline

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  39. Add the basic metrics pipeline

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  40. Introduced the concept of pipeline, auto params for all sub workflows

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  41. Added CDSFlow to metrics pipeline.

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  42. Add the possibility to save some pam values standalone

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  43. Add csa model to reconst

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  44. Small fixes to pipelines

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  45. Cleaned and fixed imports and some minor pep8 issues

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  46. Fixed a lot of pep8 warnings

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  47. Generalized the odf flow name to fit the new model switch reality

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  48. Changed quick flow name

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  49. Split fodf reconstructions, will refact l8er

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  50. Added documentation, made getting io_it even easier

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  51. Quick fix for new io_it getter.

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  52. Fixed extra param in recons csa, properly pass force param

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  53. Renamed affine to affine_to_rasm

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  54. Added a workflow creation example

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  55. Tests update wip

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  56. Continuing tests wip

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  57. Tests for combined workflow, iap and flow runner

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  58. Finished multi_io tests

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  59. Rewrote a quick method for basename without extension

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  60. Added examples for workflow and combined workflow

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  61. Add workflows examples to the lists

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  62. Better pipelines names

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  63. Fix small rebase mixup

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  64. Add shortname system to avoid samen ame params on combined workflows

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  65. Fix tests with new shortname convention

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  66. Added docstring for workflow class

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  67. Fixed typos and some code styling

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  68. Fixed some python3 errors

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  69. Fix more python3 errors

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  70. Newer version of get_io_iterator compatible with all pythons.

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  71. Removed last ref to streamlines

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  72. Temporary remove all streamline related workflows. 

    Conflicts:
	dipy/workflows/track_metrics.py
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  73. Removed streamline refs

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  74. Fix setup

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  75. Multiple review fixes, mostly docstring related

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  76. Added dipy.io.image for easy image loading

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  77. Now using dipy.image.io save/load images

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  78. Review comments - added returns in docstrings

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  79. Bunch of docstring fixes

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  80. Changed last_generated_outputs management to a more user friendly ver… 

    …sion

Conflicts:
	dipy/workflows/denoise.py
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  81. Fixed force

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  82. Fix pipelines with the new last_generated_outputs

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  83. fix the test with the new last_generated_outputs

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  84. Fixed failing test

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  85. Removed deprecated use of getargspec in python > 3

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  86. Fixed shebangs, added nlmeans to setup 

    Conflicts:
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  87. Review fixes

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  88. dti workflow first version

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  89. Samll fix to output path mecanics

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  90. Add simple pipeline

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  91. Renamed workflow to workflows

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  92. fixed remaining workflow path

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  93. All parts of the basic workflow now done.

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  94. Simple pipeline

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  95. Fixed bad name for median_otsu

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  96. Changes from introducing workflows review

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  97. New det trackin and nlm denoise

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  98. Adjusted pipeline to include denoising and new tracking

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  99. Add bin copies

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  100. Removed py ext for EuDX

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  101. Adjusted nlmeans sigma param to float

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  102. Readjust after merge

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  103. Readjust with master

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  104. Arranged denoise workflow

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  105. WIP reconst

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  106. DTI Metrics workflow

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  107. fodf and eudx tracking workflows

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  108. Deterministic tracking and TDI workflows

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  109. Added simple pipeline

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  110. Added resume parameter

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  111. Moved repetitive code own file

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  112. Removed / added blanklines

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  113. Changed multiple 'tract' for 'track'

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  114. Added basic logging

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  115. Added logging parameters to all workflows

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  116. Updated chmod

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  117. Made bool args is flags instead of v0 1 values

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  118. Fixed tests with new flaglike optionnal bools

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  119. Fixed resume, fixed fodf print crashes

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  120. Fixed nlmeans sigma help, fixed some default paths

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  121. Make dti metrics mask optionnal

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  122. Mask not mandatory anymore for fodf

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  123. Added manual fodf response function param

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  124. Removed ref in eudx tracking, comments summray in argparse

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  125. Fixed tdi with scales != 1.0

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  126. Logged upsampling factor properly

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  127. Fixed couple bugs with the pipeline

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  128. Swapped trackings in the simple_pipeline

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  129. Add references section

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  130. Added new file of supporting multiple IO

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  131. TEST: adding tests with different cases of inputs and outputs

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  132. New output params placement and naming

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  133. Output arguments now have their own section in help display

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  134. Small fix to output section name

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  135. Fixed missing tracking method out naming

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  136. Many inputs to many output tests added

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  137. New object for generating correct outputs of multiple inputs

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  138. When all sets of inputs have the same size it seems the OutputGenerat… 

    …or does the job!
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  139. TEST: testing single input

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  140. Modified track outputs to fit the new nibabel steamlines io

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  141. Removed deprecated calls to dipy

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  142. WIP on using new nibabel load on dti

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  143. TEST: adding asserts of outputs shape

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  144. NF: new class that allows generating specific filenames of outputs gi… 

    …ven any combination of one or multiple inputs of multiple subjects
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  145. DOC: small correction in explanation of OutputCreator

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  146. Fixed TDI with the new tractogram io

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  147. Adding keep input structure parameter

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  148. Added concatanation of directories to create strings

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  149. TEST: added printouts of out_dir

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  150. TEST: reduced print statements

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  151. Renamed OutputCreator to IOIterator

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  152. Add single line creation and tests

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  153. Add logging consistency test

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  154. Removed explicit path in test

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  155. Add quick load for images

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  156. Simple nifti save + test

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  157. WIP introspective IOIterator creator

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  158. made two lines one line

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  159. Slight fixes to io_iterator, pipeline wip

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  160. Implemented io_iterator in all workflows except pipeline

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  161. wip on output paths generation

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  162. NF: save/load peaks as NPZ

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  163. NF: new CSD workflow that generates peaks

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  164. NF: new deterministic tracking flow. Hopefully simpler than before. T… 

    …he input now is PeaksAndMetrics!
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  165. RF: renamed bin file for deterministic tracking

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  166. BF: wrong flow corrected in dipy_reconst_csd

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  167. BF: had to remove some inputs

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  168. BF: I had to save the vertices of the sphere from peaks not the entir… 

    …e Sphere object. You can only save arrays in .npz files. I think.
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  169. Continue working on output gen

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  170. io_iterator now creates directories

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  171. Reworked io_iterator, tests are still wip

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  172. minor updates in flows

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  173. Fixed io_iterator_ calls in flows

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  174. RF: cleaning up older tracking code

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  175. NF: added workflow for masking images

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  176. Updated tracking with an extra input of a seed mask

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  177. BF: corrected path in of seeding_mask

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  178. Corrected typos

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  179. Delete old and unmaintained binary files

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  180. Implemented workflow as objects

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  181. Fixed scripts

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  182. Fixed scripts again

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  183. Added force mecanic, finished implementing new pipeline

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  184. Completed new pipeline

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  185. test for install and quick pipeline

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  186. Moved flow_runner in dipy.workflow, makes more sense.

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  187. Fixed streamline save problem

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  188. Added skip mechanic, fancied the pipeline directories creation.

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  189. Fixed TDI out_directory in the pipeline

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  190. Add the basic metrics pipeline

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  191. Introduced the concept of pipeline, auto params for all sub workflows

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  192. Added CDSFlow to metrics pipeline.

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  193. Add the possibility to save some pam values standalone

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  194. Add csa model to reconst

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  195. Small fixes to pipelines

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  196. Cleaned and fixed imports and some minor pep8 issues

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  197. Fixed a lot of pep8 warnings

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  198. Generalized the odf flow name to fit the new model switch reality

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  199. Changed quick flow name

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  200. Split fodf reconstructions, will refact l8er

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  201. Added documentation, made getting io_it even easier

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  202. Quick fix for new io_it getter.

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  203. Fixed extra param in recons csa, properly pass force param

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  204. Renamed affine to affine_to_rasm

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  205. Added a workflow creation example

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  206. Tests update wip

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  207. Continuing tests wip

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  208. Tests for combined workflow, iap and flow runner

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  209. Finished multi_io tests

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  210. Rewrote a quick method for basename without extension

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  211. Added examples for workflow and combined workflow

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  212. Add workflows examples to the lists

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  213. Better pipelines names

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  214. Fix small rebase mixup

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  215. Add shortname system to avoid samen ame params on combined workflows

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  216. Fix tests with new shortname convention

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  217. Added docstring for workflow class

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  218. Fixed typos and some code styling

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  219. Fixed some python3 errors

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  220. Fix more python3 errors

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  221. Newer version of get_io_iterator compatible with all pythons.

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  222. Removed last ref to streamlines

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  223. Temporary remove all streamline related workflows. 

    Conflicts:
	dipy/workflows/track_metrics.py
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  224. Removed streamline refs

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  225. Fix setup

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  226. Multiple review fixes, mostly docstring related

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  227. Added dipy.io.image for easy image loading

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  228. Now using dipy.image.io save/load images

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  229. Review comments - added returns in docstrings

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    matthieudumont committed Aug 30, 2016
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  230. Bunch of docstring fixes

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  231. Changed last_generated_outputs management to a more user friendly ver… 

    …sion

Conflicts:
	dipy/workflows/denoise.py
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  232. Fixed force

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    matthieudumont committed Aug 30, 2016
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  233. Fix pipelines with the new last_generated_outputs

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    matthieudumont committed Aug 30, 2016
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  234. fix the test with the new last_generated_outputs

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    matthieudumont committed Aug 30, 2016
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  235. Fixed failing test

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    matthieudumont committed Aug 30, 2016
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  236. Removed deprecated use of getargspec in python > 3

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  237. Fixed shebangs, added nlmeans to setup 

    Conflicts:
	setup.py
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  238. Fixed Shebangs

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    matthieudumont committed Aug 30, 2016
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Commits on Sep 16, 2016

  1. Merged with current master

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    matthieudumont committed Sep 16, 2016
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  2. Merged with recent master

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    matthieudumont committed Sep 16, 2016
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Commits on Sep 22, 2016

  1. Fixed some merge stuff left in example doc

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    matthieudumont committed Sep 22, 2016
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  2. Fixed python lin

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    matthieudumont committed Sep 22, 2016
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  3. Added the reconst_dti flow

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    matthieudumont committed Sep 22, 2016
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  4. Added det tracking back

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    matthieudumont committed Sep 22, 2016
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  5. Forgot the actual tracking workflow

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    matthieudumont committed Sep 22, 2016
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  6. Add the track_density workflow

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    matthieudumont committed Sep 22, 2016
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  7. Cleaned for dti reconst only

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    matthieudumont committed Sep 22, 2016
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  8. forgot to remove mask

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    matthieudumont committed Sep 22, 2016
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  9. Refixed shebangs

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    matthieudumont committed Sep 22, 2016
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Commits on Sep 23, 2016

  1. Last clean for recons_dti_only branch

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    matthieudumont committed Sep 23, 2016
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