rapidtide 3.0.4__tar.gz → 3.0.5__tar.gz

{rapidtide-3.0.4 → rapidtide-3.0.5}/CHANGELOG.md

@@ -1,5 +1,8 @@
 # Release history
 
+## Version 3.0.5 (5/7/25)
+* (rapidtide) Loosened the sample rate matching when appending timecourses to files, and read NIFTI tr values using modern header features.  This should help address https://github.com/bbfrederick/rapidtide/issues/205 (thank you to https://github.com/phildeming for finding this).
+
 ## Version 3.0.4 (5/5/25)
 * (rapidtide, retrotregress, tidepool) Support for maxcorrrefined map.
 * (retroregress) Gracefully handles missing mask names in runoptions file.

{rapidtide-3.0.4/rapidtide.egg-info → rapidtide-3.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.4
+Version: 3.0.5
 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>

{rapidtide-3.0.4 → rapidtide-3.0.5}/rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-05-06T11:02:28-0400",
+ "date": "2025-05-07T20:47:14-0400",
  "dirty": false,
  "error": null,
- "full-revisionid": "c5e5e2f38938a78c3439882e8ad596c483c6adcf",
- "version": "3.0.4"
+ "full-revisionid": "ea9d8f413eaa094534d2da7318765380528980fe",
+ "version": "3.0.5"
 }
 '''  # END VERSION_JSON
 

{rapidtide-3.0.4 → rapidtide-3.0.5}/rapidtide/io.py

@@ -1426,6 +1426,8 @@ def writebidstsv(
     yaxislabel="arbitrary value",
     starttime=0.0,
     append=False,
+    samplerate_tolerance=1e-6,
+    starttime_tolerance=1e-6,
     colsinjson=True,
     colsintsv=False,
     omitjson=False,
@@ -1498,8 +1500,8 @@ def writebidstsv(
                 )
             compressed = incompressed
             if (
-                (insamplerate == samplerate)
-                and (instarttime == starttime)
+                np.fabs(insamplerate - samplerate) < samplerate_tolerance
+                and np.fabs(instarttime - starttime) < starttime_tolerance
                 and reshapeddata.shape[1] == indata.shape[1]
             ):
                 startcol = len(incolumns)

{rapidtide-3.0.4 → rapidtide-3.0.5}/rapidtide/workflows/rapidtide_parser.py

@@ -1916,7 +1916,7 @@ def process_args(inputargs=None):
 
     if args["in_file"].endswith("txt") and args["realtr"] == "auto":
         raise ValueError(
-            "Either --datatstep or --datafreq must be provided " "if data file is a text file."
+            "Either --datatstep or --datafreq must be provided if data file is a text file."
         )
 
     if args["realtr"] != "auto":
@@ -1925,7 +1925,7 @@ def process_args(inputargs=None):
         if tide_io.checkifcifti(args["in_file"]):
             fmri_tr, dummy = tide_io.getciftitr(nib.load(args["in_file"]).header)
         else:
-            fmri_tr = nib.load(args["in_file"]).header.get_zooms()[3]
+            fmri_tr, dummy = tide_io.fmritimeinfo(args["in_file"])
     args["realtr"] = fmri_tr
 
     if args["inputfreq"] == "auto":

{rapidtide-3.0.4 → rapidtide-3.0.5}/rapidtide/workflows/simdata.py

@@ -53,46 +53,44 @@ def _get_parser():
 
     for band in ["lfo", "resp", "cardiac"]:
         parser.add_argument(
-            "--" + band + "pctfile",
-            dest=(band + "pctfile"),
+            f"--{band}pctfile",
+            dest=(f"{band}pctfile"),
             action="store",
             type=lambda x: pf.is_valid_file(parser, x),
             metavar="FILE",
-            help=(
-                "3D NIFTI file with the " + band + " amplitude in percent of mean at every point"
-            ),
+            help=(f"3D NIFTI file with the {band} amplitude in percent of mean at every point"),
             default=None,
         )
         parser.add_argument(
-            "--" + band + "lagfile",
-            dest=(band + "lagfile"),
+            f"--{band}lagfile",
+            dest=(f"{band}lagfile"),
             action="store",
             type=lambda x: pf.is_valid_file(parser, x),
             metavar="FILE",
-            help=("3D NIFTI file with the " + band + " delay value in seconds at every point"),
+            help=(f"3D NIFTI file with the {band} delay value in seconds at every point"),
             default=None,
         )
         parser.add_argument(
-            "--" + band + "regressor",
-            dest=(band + "regressor"),
+            f"--{band}regressor",
+            dest=(f"{band}regressor"),
             action="store",
             type=lambda x: pf.is_valid_file(parser, x),
             metavar="FILE",
-            help=("The LFO regressor text file"),
+            help=(f"The {band} regressor text file"),
             default=None,
         )
         parser.add_argument(
-            "--" + band + "samprate",
-            dest=(band + "samprate"),
+            f"--{band}samprate",
+            dest=(f"{band}samprate"),
             action="store",
             type=float,
             metavar="SAMPRATE",
-            help=("The sample rate of the LFO regressor file, in Hz"),
+            help=(f"The sample rate of the {band} regressor file, in Hz"),
             default=None,
         )
         parser.add_argument(
-            "--" + band + "starttime",
-            dest=(band + "starttime"),
+            f"--{band}starttime",
+            dest=(f"{band}starttime"),
             action="store",
             type=float,
             metavar="STARTTIME",
@@ -317,7 +315,7 @@ def simdata(args):
         sliceoffsettimes *= fmritr
 
     nim_fmri, fmridata, fmriheader, fmridims, fmrisizes = tide_io.readfromnifti(args.fmrifilename)
-    print("fmri data: ", numtrs, " timepoints, tr = ", fmritr)
+    print(f"fmri data: {numtrs} timepoints, tr = {fmritr}")
 
     # prepare the output timepoints
     initial_fmri_x = (
@@ -328,12 +326,8 @@ def simdata(args):
     )
     print("length of fmri after removing skip:", len(initial_fmri_x))
     print(
-        "fmri time has length",
-        len(initial_fmri_x),
-        "and runs runs from ",
-        initial_fmri_x[0],
-        " to ",
-        initial_fmri_x[-1],
+        f"fmri time has length {len(initial_fmri_x)}",
+        f"and runs runs from {initial_fmri_x[0]} to {initial_fmri_x[-1]}",
     )
 
     # read in the immean file

{rapidtide-3.0.4 → rapidtide-3.0.5/rapidtide.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.0.4
+Version: 3.0.5
 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>