Merge pull request #65 from arokem/refactor_segmentation

Refactor segmentation for speedup
yeatmanlab · May 26, 2018 · 02c68a2 · 02c68a2
2 parents 027ddba + 172892c
commit 02c68a2
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Showing 6 changed files with 440 additions and 109 deletions.
diff --git a/AFQ/data.py b/AFQ/data.py
@@ -92,97 +92,151 @@ def read_callosum_templates():
                    "ATR_roi1_R.nii.gz",
                    "ATR_roi2_L.nii.gz",
                    "ATR_roi2_R.nii.gz",
+                   "ATR_L_prob_map.nii.gz",
+                   "ATR_R_prob_map.nii.gz",
                    "CGC_roi1_L.nii.gz",
                    "CGC_roi1_R.nii.gz",
                    "CGC_roi2_L.nii.gz",
                    "CGC_roi2_R.nii.gz",
+                   "CGC_L_prob_map.nii.gz",
+                   "CGC_R_prob_map.nii.gz",
                    "CST_roi1_L.nii.gz",
                    "CST_roi1_R.nii.gz",
                    "CST_roi2_L.nii.gz",
                    "CST_roi2_R.nii.gz",
+                   "CST_L_prob_map.nii.gz",
+                   "CST_R_prob_map.nii.gz",
                    "FA_L.nii.gz",
                    "FA_R.nii.gz",
+                   "FA_prob_map.nii.gz",
                    "FP_L.nii.gz",
                    "FP_R.nii.gz",
+                   "FP_prob_map.nii.gz",
                    "HCC_roi1_L.nii.gz",
                    "HCC_roi1_R.nii.gz",
                    "HCC_roi2_L.nii.gz",
                    "HCC_roi2_R.nii.gz",
+                   "HCC_L_prob_map.nii.gz",
+                   "HCC_R_prob_map.nii.gz",
                    "IFO_roi1_L.nii.gz",
                    "IFO_roi1_R.nii.gz",
                    "IFO_roi2_L.nii.gz",
                    "IFO_roi2_R.nii.gz",
+                   "IFO_L_prob_map.nii.gz",
+                   "IFO_R_prob_map.nii.gz",
                    "ILF_roi1_L.nii.gz",
                    "ILF_roi1_R.nii.gz",
                    "ILF_roi2_L.nii.gz",
                    "ILF_roi2_R.nii.gz",
+                   "ILF_L_prob_map.nii.gz",
+                   "ILF_R_prob_map.nii.gz",
                    "SLF_roi1_L.nii.gz",
                    "SLF_roi1_R.nii.gz",
                    "SLF_roi2_L.nii.gz",
                    "SLF_roi2_R.nii.gz",
                    "SLFt_roi2_L.nii.gz",
                    "SLFt_roi2_R.nii.gz",
+                   "SLF_L_prob_map.nii.gz",
+                   "SLF_R_prob_map.nii.gz",
                    "UNC_roi1_L.nii.gz",
                    "UNC_roi1_R.nii.gz",
                    "UNC_roi2_L.nii.gz",
-                   "UNC_roi2_R.nii.gz"]
+                   "UNC_roi2_R.nii.gz",
+                   "UNC_L_prob_map.nii.gz",
+                   "UNC_R_prob_map.nii.gz",
+                   "ARC_L_prob_map.nii.gz",
+                   "ARC_R_prob_map.nii.gz"]
+
 
 template_remote_fnames = ["5273680", "5273683", "5273686", "5273689",
+                          "11458274", "11458277",
                           "5273695", "5273692", "5273698", "5273701",
+                          "11458268", "11458271",
                           "5273704", "5273707", "5273710", "5273713",
-                          "5273716", "5273719", "5273722", "5273725",
+                          "11458262", "11458265",
+                          "5273716", "5273719",
+                          "11458220",
+                          "5273722", "5273725",
+                          "11458226",
                           "5273728", "5273731", "5273734", "5273746",
+                          "11458259", "11458256",
                           "5273737", "5273740", "5273743", "5273749",
+                          "11458250", "11458253",
                           "5273752", "5273755", "5273758", "5273761",
+                          "11458244", "11458247",
                           "5273764", "5273767", "5273770", "5273773",
-                          "5273776", "5273791", "5273779", "5273782",
-                          "5273785", "5273788"]
+                          "5273776", "5273791",
+                          "11458238", "11458241",
+                          "5273779", "5273782", "5273785", "5273788",
+                          "11458223", "11458229",
+                          "11458232", "11458235"]
 
 
 template_md5_hashes = ["6b7aaed1a2982fd0ea436a223133908b",
                        "fd60d46d4e3cbd906c86e4c9e4fd6e2a",
                        "3aba60b169a35c38640de4ec29d362c8",
                        "12716a5688a1809fbaed1d58d2e68b59",
+                       "c5637f471df861d9bbb45604db34770b",
+                       "850cc4c04d7241747063fe3cd440b2ce",
                        "8e8973bc7838c8744914d402f52d91ca",
                        "c5fa4e6e685e695c006823b6784d2407",
                        "e1fab77f21d5303ed52285f015e24f0b",
                        "5f89defec3753fd75cd688c7bfb20a36",
+                       "a4f3cd65b06fb25f63d5dab7592f00f2",
+                       "7e73ab02db30a3ad6bd9e82148c2486e",
                        "f9db3154955a20b67c2dda758800d14c",
                        "73941510c798c1ed1b03e2bd481cd5c7",
                        "660cdc031ee0716d60159c7d933119ea",
                        "660cdc031ee0716d60159c7d933119ea",
+                       "fd012bc89f6bed7bd54530195496bac4",
+                       "3406906a86e633cc102127cf210a1063",
                        "9040a7953dcbbf131d135c866182d8ef",
                        "a72e17194824fcd838a594a2eb50c72e",
+                       "627d7bb2e6d55f8243da815a36d9ff1a",
                        "55adbe9b8279185eedbe342149e1ff90",
                        "5a7412a3cf0fb185eec53d1989df2f7c",
+                       "1aa36e83ae7b5555bb19d776ede9c18d",
                        "ba453196ff179b0e31172806e313b52c",
                        "d85c6574526b296935f34bf4f65cd493",
                        "9b81646317f59c7db087f27e2f85679e",
                        "9806e82c250e4604534b96917f87b7e8",
+                       "213d3fb1ccd756d878f9b50b765b1c8f",
+                       "f1e7e6bc51aa0aa279c54fb3805fb5e3",
                        "0e68a9feaaddcc9b4d667c2f15903368",
                        "d45020a87ee4bb496edd350631d91f6a",
                        "75c2c911826ec4b23159f9bd80e3c039",
                        "55d616ea9e0c646adc1aafa0f5fbe625",
+                       "dee83fa6b03cfa5e0f5c965953aa6778",
+                       "a13eef7059c98568adfefbab660e434e",
                        "045b7d5c6341997f3f0120c3a4212ad8",
                        "d174b1359ba982b03840436c93b7bbb4",
                        "fff9753f394fc4c73fb2ae40b3b4dde0",
                        "cd278b4dd6ff77481ea9ac16485a5ae2",
+                       "7bdf5111265107091c7a2fca9215de30",
+                       "7d4a43714504e6e930f922c9bc2a13d5",
                        "af2bcedf47e193686af329b9a8e259da",
                        "9a1122943579d11ba169d3ad87a75625",
                        "627903f7a06627bfd4153dc9245fa390",
                        "1714cd7f989c3435bdd5a2076e6272a0",
                        "1fa2114049707a4e05b53f9d95730375",
                        "b6663067d5ea53c70cb8803948f8adf7",
+                       "d3e068997ebc60407bd6e9576e47dede",
+                       "27ecfbd1d2f98213e52d73b7d70fe0e7",
                        "fa141bb2d951bec486916acda3652d95",
                        "d391d073e86e28588be9a6d01b2e7a82",
                        "a3e085562e6b8111c7ebc358f9450c8b",
-                       "d65c67910807504735e034f7ea92d590"]
+                       "d65c67910807504735e034f7ea92d590",
+                       "93cb24a9128db1a6c34a09eaf79fe7f0",
+                       "71a7455cb4062dc39b1677c118c7b5a5",
+                       "19590c712f1776da1fdba64d4eb7f1f6",
+                       "04d5af0feb2c1b5b52a87ccbbf148e4b",
+                       "53c277be990d00f7de04f2ea35e74d73"]
 
 fetch_templates = _make_fetcher("fetch_templates",
                                 op.join(afq_home, 'templates'),
                                 baseurl, template_remote_fnames,
                                 template_fnames, md5_list=template_md5_hashes,
-                                doc="Download AFQ callosum templates")
+                                doc="Download AFQ templates")
 
 
 def read_templates():