rapidtide 3.0.10__py3-none-any.whl → 3.0.11__py3-none-any.whl

rapidtide/OrthoImageItem.py

@@ -137,6 +137,7 @@ class OrthoImageItem(QtWidgets.QWidget):
     ):
         QtWidgets.QWidget.__init__(self)
         self.map = map
+        self.mapname = self.map.label
         self.bgmap = bgmap
         self.axview = axview
         self.corview = corview
@@ -180,6 +181,7 @@ class OrthoImageItem(QtWidgets.QWidget):
 
         if self.verbose > 1:
             print("OrthoImageItem initialization:")
+            print("    Map name:", self.mapname)
             print("    Dimensions:", self.xdim, self.ydim, self.zdim)
             print("    Voxel sizes:", self.xsize, self.ysize, self.zsize)
             print("    FOVs:", self.xfov, self.yfov, self.zfov)
@@ -361,6 +363,7 @@ class OrthoImageItem(QtWidgets.QWidget):
     def setMap(self, themap):
         self.map = themap
         self.tdim = self.map.tdim
+        self.mapname = self.map.label
 
     def enableView(self):
         if self.button is not None:

rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-08-18T17:30:20-0400",
+ "date": "2025-08-27T10:21:33-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "939d31d88a5839ee746b0f84f4d370248fe5b312",
- "version": "3.0.10"
+ "full-revisionid": "078ea587f66134f5bb1f53817240da52156cf7f1",
+ "version": "3.0.11"
 }
 '''  # END VERSION_JSON
 

rapidtide/data/examples/src/testhappy

@@ -72,5 +72,12 @@
 happy \
     sub-HAPPYTEST.nii.gz \
     sub-HAPPYTEST.json \
-    ../dst/happy_newdefaults \
+    ../dst/happy_mask \
+    --processmask sub-HAPPYTEST_mask.nii.gz \
+    --nprocs -1
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy \
     --nprocs -1

rapidtide/fit.py

@@ -258,7 +258,7 @@ def trapezoid_eval(x, toplength, p):
 
     The trapezoidal function is defined as:
 
-    f(x) = A \* (1 - exp(-x / tau))
+    f(x) = A * (1 - exp(-x / tau))
 
     if 0 <= x < L
 

rapidtide/workflows/happy.py

@@ -24,7 +24,6 @@ import warnings
 from pathlib import Path
 
 import numpy as np
-from scipy.stats import pearsonr
 
 import rapidtide.correlate as tide_corr
 import rapidtide.filter as tide_filt
@@ -195,7 +194,18 @@ def happy_main(argparsingfunc):
 
     # make and save a mask of the voxels to process based on image intensity
     tide_util.logmem("before mask creation")
-    mask = np.uint16(tide_mask.makeepimask(input_data.nim).dataobj.reshape(numspatiallocs))
+    if args.processmask is not None:
+        mask = tide_mask.readamask(
+            args.processmask,
+            input_data.copyheader(numtimepoints=1),
+            xsize,
+            maskname="process",
+            debug=args.debug,
+        )
+        mask = np.uint16(np.where(mask > 0, 1, 0).reshape(numspatiallocs))
+    else:
+        mask = np.uint16(tide_mask.makeepimask(input_data.nim).dataobj.reshape(numspatiallocs))
+
     theheader = input_data.copyheader(numtimepoints=1)
     timings.append(["Mask created", time.time(), None, None])
     if args.outputlevel > 0:

rapidtide/workflows/happy_parser.py

@@ -556,6 +556,18 @@ def _get_parser():
 
     # Add miscellaneous options
     misc_opts = parser.add_argument_group("Miscellaneous options.")
+    misc_opts.add_argument(
+        "--processmask",
+        dest="processmask",
+        action="store",
+        metavar="MASKNAME",
+        help=(
+            "Instead of dynamically generating a processing mask from the data, use "
+            "the mask specified in the file MASKNAME. "            
+            "The mask must be a 3D NIFTI file with x, y, z dimensions matching the fMRI data. "
+        ),
+        default=None,
+    )
     misc_opts.add_argument(
         "--aliasedcorrelation",
         dest="doaliasedcorrelation",

rapidtide/workflows/tidepool.py

@@ -2052,19 +2052,19 @@ def tidepool(args):
         },
         "varBefore": {
             "colormap": gen_thermal_state(),
-            "label": "LFO variance before filtering",
+            "label": "LFO var. before filtering",
             "display": extramaps,
             "funcmask": "p_lt_0p050_mask",
         },
         "varAfter": {
             "colormap": gen_thermal_state(),
-            "label": "LFO variance after filtering",
+            "label": "LFO var. after filtering",
             "display": extramaps,
             "funcmask": "p_lt_0p050_mask",
         },
         "varChange": {
             "colormap": gen_thermal_state(),
-            "label": "LFO variance decrease %",
+            "label": "LFO var. decrease %",
             "display": True,
             "funcmask": "p_lt_0p050_mask",
         },

{rapidtide-3.0.10.dist-info → rapidtide-3.0.11.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.10
+Version: 3.0.11
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>
@@ -42,13 +42,13 @@ Requires-Dist: tensorflow>=2.18.0
 Requires-Dist: tf-keras>=2.18.0
 Requires-Dist: tqdm
 Requires-Dist: versioneer
-Provides-Extra: tests
-Requires-Dist: codecov; extra == "tests"
-Requires-Dist: coverage; extra == "tests"
-Requires-Dist: coveralls; extra == "tests"
-Requires-Dist: flake8-black; extra == "tests"
-Requires-Dist: pytest; extra == "tests"
-Requires-Dist: pytest-cov; extra == "tests"
+Provides-Extra: test
+Requires-Dist: codecov; extra == "test"
+Requires-Dist: coverage; extra == "test"
+Requires-Dist: coveralls; extra == "test"
+Requires-Dist: flake8-black; extra == "test"
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
 Provides-Extra: doc
 Requires-Dist: sphinx; extra == "doc"
 Requires-Dist: sphinx_rtd_theme; extra == "doc"

{rapidtide-3.0.10.dist-info → rapidtide-3.0.11.dist-info}/RECORD

@@ -7,10 +7,10 @@ cloud/rapidtide-HCPYA,sha256=kqW8ENbOQhvVqZGz-HqiVbrbzHy4cfyy1rk8ejpJor0,963
 cloud/rapidtide-cloud-test,sha256=SATOwGo4QYLvt-6hE0e3wyK9JjuDU5XzfLrfMoybvcY,466
 cloud/simple-cp-test,sha256=5ef8wmLfcKdny59BV6_DnAPj7O_mi0rOHdFZVN2iiLA,421
 rapidtide/Colortables.py,sha256=OVtgnQ9xTJPgfdyK1ktESHRjBh09cxLVPZvgUvV5jOo,5814
-rapidtide/OrthoImageItem.py,sha256=BVvIPtx8rCjk2vDCDYOILJYSEfrDZtLK19Facz59Gyc,21974
+rapidtide/OrthoImageItem.py,sha256=bF4-2zeYdBpFLo88Xh9_YP77rPO2iZUXYIW1-fISyfA,22099
 rapidtide/RapidtideDataset.py,sha256=HNo20XDA5UX8uErL43XCsn3LtqPmfeBDJplOeESSNho,53526
 rapidtide/__init__.py,sha256=cECnPfGNIWXETiummGLjKcNXLROSDiFlLp-RpZSavwc,97
-rapidtide/_version.py,sha256=Ns5TcocXs50JS4gK337_iat2ybvs5LnpSO11KL_PZrE,498
+rapidtide/_version.py,sha256=VpdusWoveo4WzCtORlRLO4_cUPh967EA-ngtS9BSCW8,498
 rapidtide/calccoherence.py,sha256=-_vglu0MZB85Aodw6GpYhBApFBt5eslppfxF4rXM6Xg,3409
 rapidtide/calcnullsimfunc.py,sha256=j5mPfaRCpJvu8R-kHFzn6vrIQVhCdPPDTSYXslaZU_c,5030
 rapidtide/calcsimfunc.py,sha256=xCPYns-XOnLWjwujbP7a7EwGEzhEwOHMf04RpFlL3SI,4713
@@ -19,7 +19,7 @@ rapidtide/dlfilter.py,sha256=sJ1UoekNFlGVJOIeN6BKP_-pU-MOHD5Gc4GT7FTB2So,58161
 rapidtide/externaltools.py,sha256=-p2GZRRpI2_7eRY8N6lnG4DBQKoRd_WZZQzvgFCicUY,3965
 rapidtide/fMRIData_class.py,sha256=ELJf7iHkLUjASiZRekdY6Zafsq1RHsH0htITrBepYpY,4448
 rapidtide/filter.py,sha256=ErHjV3tj3R-Q02kGFksIviKda65y1xB_9MR1Cip1uho,70231
-rapidtide/fit.py,sha256=VPuc-Lwt3kuNgRj0pu32hfz9cRUBLcJk1PJbX4gonxc,90100
+rapidtide/fit.py,sha256=C2V7qG0jZ5NjZ8xEwx5xbWPohIeDeqjL66dCdFlQT2Y,90099
 rapidtide/genericmultiproc.py,sha256=ZQwN84HpC7ZA_w4qekBqA4suU_70ryqGjAsTAIa4oSw,3423
 rapidtide/happy_supportfuncs.py,sha256=GiUwfjf0ZIYEvN2Fvauhtv58hdiAuQytwx11ZPX8Uvo,56261
 rapidtide/helper_classes.py,sha256=14q92myZQPl_AUTjh5l1dm6y5-3JkW0xCAEKpgyiuXY,10534
@@ -70,7 +70,7 @@ rapidtide/data/examples/src/testfmridocker,sha256=jjL7bK29rrcog6uO9BtvcyAU3Sv8_5
 rapidtide/data/examples/src/testfrozen,sha256=K3qUWDRKPPiCXRgIFuPdwUUjUTzf4QBW8UUhR75NzDM,283
 rapidtide/data/examples/src/testfuncs,sha256=zjq9u7mXMf0UlbUgePyS1mj7QHclicmw6NY0g31SqeY,1551
 rapidtide/data/examples/src/testglmfilt,sha256=MuZlVBJIV7FrTWFLKGuWBcpR9WiZEjCGeD6cAnJLeNI,3357
-rapidtide/data/examples/src/testhappy,sha256=bH2pYc60BtpS1OkbFfmsrvc50pN84lnOI6sPqjkMfaQ,1530
+rapidtide/data/examples/src/testhappy,sha256=d625dqMgzuzieuV5J9UDEp55DtMORnw_e1BNvgOfSAs,1665
 rapidtide/data/examples/src/testinitdelay,sha256=ts_r5WZBLJDQ3UfPmJ9sfXlO0arO9dhGCQ_Y1wYvjMk,559
 rapidtide/data/examples/src/testlinfit,sha256=oPnkHJ6lcwsuJhnSMMK7Gx3DHSCf6JK7CIYuIMHbyNA,471
 rapidtide/data/examples/src/testlocalflow,sha256=hEwstisbWVuALr_29fBJ2nHETKkEF_9qK8wJ4kzuiJk,596
@@ -129,6 +129,8 @@ rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_regions.txt,sha
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1-seg2_space-MNI152NLin6Asym_2mm.nii.gz,sha256=xIM9iAo1ztHAH0ihbwYMWw7C_px7HSN11DmENtpUA94,167371
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1.xml,sha256=rBCJlGbYkquJJogj4AXd-RQspCW8Zdp_gyJaHKrC7D0,5563
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_regions.txt,sha256=7ESGMqBtDNFcO3So9h22o1-B2CfBA0kD3hjCJ5tpnFU,160
+rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm.nii.gz,sha256=2C2ki5IKk_ONSQKR1EO827ztdYo_5X6iAeFmtI09zmI,58100
+rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin2009cAsym_2mm_mask.nii.gz,sha256=7aFfHRz3R-Ox2rp8bY_Fdb30V-gJAbQu6mZAmvIGCs0,42333
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin6Asym_2mm.nii.gz,sha256=59jvK4oRbBwXr2hLvkMrFhg7D1mhQqB_iE7w2UeHwzE,123094
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL1_space-MNI152NLin6Asym_2mm_mask.nii.gz,sha256=czFxUYChXvCpA8USfghVK-NMB1JpBGHujrSq23BwvCE,38701
 rapidtide/data/reference/JHU-ArterialTerritoriesNoVent-LVL2.xml,sha256=ay_Dm2R8FFbwTXau7MPGQhSVK_d1zgD6S6GxR7W_YzY,3351
@@ -306,9 +308,9 @@ rapidtide/workflows/filttc.py,sha256=QHMJ41ZORxB8fG4IcvxKUgSfmOL4X9cFQFpM5px1Uxw
 rapidtide/workflows/fitSimFuncMap.py,sha256=SwyOs8QJHEB8QK6GwKLrGvhg9Cc0wpqYgGt9L1mXB00,16711
 rapidtide/workflows/fixtr.py,sha256=KYr3veeHDUjozH3IO-0iPhLqNDGEc2NcUvzn6tuxeN8,2025
 rapidtide/workflows/gmscalc.py,sha256=Z-3HV2EU-HuIhpr7s5u4EAPAaW0gXtj2aVZt7386Gr8,6258
-rapidtide/workflows/happy.py,sha256=jx3YgNfwIbKLdawilyoirrb0mNLrWJJdKiVC_tywBXk,77204
+rapidtide/workflows/happy.py,sha256=YMcQ5ji5_ggjOUoryRmk1V0cIX7k1oW40WXVn5H2C6o,77507
 rapidtide/workflows/happy2std.py,sha256=6gya9YjfPzPMu15jsMUbu7pLq430-n3b3meiTWhRkAo,8132
-rapidtide/workflows/happy_parser.py,sha256=OQTcUIvB61p0niNpG__9auUINb962PKmp0wz6qj_uN8,27354
+rapidtide/workflows/happy_parser.py,sha256=ZkD3hUEcQUCz4JBTmWWR9cLYNY_CUD1x6U5asNOfai8,27791
 rapidtide/workflows/histnifti.py,sha256=BeABj0osc0mEnmyKonN0Hgeis8L8soO-w-cVaeMKLUI,11197
 rapidtide/workflows/histtc.py,sha256=ZiLLTshdpQBVHja1jEGFiaZ-YVxVhVtFeGv9w5R7HFc,4561
 rapidtide/workflows/linfitfilt.py,sha256=J6_qFZrfEf8Zf7-JA9EMaSXvyV_2ViNIqzju-ugjNGU,10007
@@ -350,12 +352,12 @@ rapidtide/workflows/spectrogram.py,sha256=7_CzFgX9ppE_2C4GiSP235BRUoh3YspCR_57_5
 rapidtide/workflows/synthASL.py,sha256=v4zkfrXbb6Y06IsAhSm3ZmL4UTPYWaK3vPnP3bKr-co,4971
 rapidtide/workflows/tcfrom2col.py,sha256=o7IEQ-YqN_VDu-f_9lme4DtSn8EbYCK5TCwGBGGr0YY,1936
 rapidtide/workflows/tcfrom3col.py,sha256=kV3V-qZ7A7LkD96aHVXabvohA8udsflHXnzsQIwiKug,1938
-rapidtide/workflows/tidepool.py,sha256=l9SNEDQaUGBGTmaFbpDHR9VDfGZlSvq1SlV6jJMS88M,87850
+rapidtide/workflows/tidepool.py,sha256=fl78xbAwyeh13du8i4lLyfeN2y-z33XNuOM2RNY6hew,87838
 rapidtide/workflows/utils.py,sha256=urIN-042oUCRDusVUSjBelVN3Te2JP3svY3ckq-yBMU,5379
 rapidtide/workflows/variabilityizer.py,sha256=h7Hhrxn84MclRfbAvKIZJoNzlcKO-8d9lZ6y6YFStk8,3167
-rapidtide-3.0.10.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
-rapidtide-3.0.10.dist-info/METADATA,sha256=V4Q_tLKVmClm1_VK6bmwluPj8gKCbrHimCxH1m5SIY8,15705
-rapidtide-3.0.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-rapidtide-3.0.10.dist-info/entry_points.txt,sha256=9NVvZpIx9U6lTWlTFF2ev-wuPAHJxcXI_901_EcGRYA,3323
-rapidtide-3.0.10.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
-rapidtide-3.0.10.dist-info/RECORD,,
+rapidtide-3.0.11.dist-info/licenses/LICENSE,sha256=psuoW8kuDP96RQsdhzwOqi6fyWv0ct8CR6Jr7He_P_k,10173
+rapidtide-3.0.11.dist-info/METADATA,sha256=enWIc3wBzPIfPFSEM6k-0elE66KJPuDzEFAlwHvRTnE,15698
+rapidtide-3.0.11.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rapidtide-3.0.11.dist-info/entry_points.txt,sha256=9NVvZpIx9U6lTWlTFF2ev-wuPAHJxcXI_901_EcGRYA,3323
+rapidtide-3.0.11.dist-info/top_level.txt,sha256=MnNXGfbrIBc9RnAqzBHOWd3GQO-aIUDnRTz4_5VjH5g,16
+rapidtide-3.0.11.dist-info/RECORD,,