rapidtide 3.0a12__py3-none-any.whl → 3.0a13__py3-none-any.whl

rapidtide/scripts/retroregress.py

@@ -0,0 +1,28 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2024 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+import rapidtide.workflows.parser_funcs as pf
+import rapidtide.workflows.retroregress as theworkflow
+
+
+def entrypoint():
+    pf.generic_init(theworkflow._get_parser, theworkflow.retroregress)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/stupidramtricks.py

@@ -29,7 +29,7 @@ import rapidtide.workflows.parser_funcs as pf
 
 def _get_parser():
     """
-    Argument parser for glmfilt
+    Argument parser for stupidramtricks
     """
     parser = argparse.ArgumentParser(
         prog="stupidramtricks",
@@ -141,7 +141,9 @@ def stupidramtricks(args):
         fmridata, fmridata_shm = tide_util.numpy2shared(
             fmridata, rt_floatset, name=f"fmridata_{args.pid}"
         )
-        glmmean, glmmean_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
+        sLFOfitmean, sLFOfitmean_shm = tide_util.allocshared(
+            internalvalidspaceshape, rt_outfloatset
+        )
         rvalue, rvalue_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
         r2value, r2value_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloatset)
         fitNorm, fitNorm_shm = tide_util.allocshared(internalvalidspaceshapederivs, rt_outfloatset)
@@ -160,7 +162,7 @@ def stupidramtricks(args):
     else:
         if args.debug:
             print("allocating memory")
-        glmmean = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
+        sLFOfitmean = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
         rvalue = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
         r2value = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
         fitNorm = np.zeros(internalvalidspaceshapederivs, dtype=rt_outfloattype)
@@ -172,7 +174,7 @@ def stupidramtricks(args):
 
     totalbytes = (
         fmridata.nbytes
-        + glmmean.nbytes
+        + sLFOfitmean.nbytes
         + rvalue.nbytes
         + r2value.nbytes
         + fitNorm.nbytes
@@ -185,7 +187,7 @@ def stupidramtricks(args):
     thesize, theunit = tide_util.format_bytes(totalbytes)
     print(f"allocated {thesize:.3f} {theunit} {location}")
 
-    """glmderivratios = tide_refinedelay.getderivratios(
+    """regressderivratios, regressrvalues = tide_refinedelay.getderivratios(
         fmri_data_valid,
         validvoxels,
         initial_fmri_x,
@@ -195,7 +197,7 @@ def stupidramtricks(args):
         mode,
         outputname,
         oversamptr,
-        glmmean,
+        sLFOfitmean,
         rvalue,
         r2value,
         fitNorm[:, :2],
@@ -212,7 +214,7 @@ def stupidramtricks(args):
     # clean up shared memory
     if args.usesharedmem:
         tide_util.cleanup_shm(fmridata_shm)
-        tide_util.cleanup_shm(glmmean_shm)
+        tide_util.cleanup_shm(sLFOfitmean_shm)
         tide_util.cleanup_shm(rvalue_shm)
         tide_util.cleanup_shm(r2value_shm)
         tide_util.cleanup_shm(fitNorm_shm)

rapidtide/simfuncfit.py

@@ -43,7 +43,7 @@ def onesimfuncfit(
 ):
     if initiallag is not None:
         thefitter.setguess(True, maxguess=initiallag)
-        thefitter.setrange(-despeckle_thresh/2.0, despeckle_thresh/2.0)
+        thefitter.setrange(-despeckle_thresh / 2.0, despeckle_thresh / 2.0)
     else:
         thefitter.setguess(False)
 

rapidtide/tests/cleanposttest

@@ -0,0 +1,21 @@
+#!/bin/sh
+#
+#   Copyright 2016-2021 Blaise Frederick
+#
+#   Licensed under the Apache License, Version 2.0 (the "License");
+#   you may not use this file except in compliance with the License.
+#   You may obtain a copy of the License at
+#
+#       http://www.apache.org/licenses/LICENSE-2.0
+#
+#   Unless required by applicable law or agreed to in writing, software
+#   distributed under the License is distributed on an "AS IS" BASIS,
+#   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#   See the License for the specific language governing permissions and
+#   limitations under the License.
+#
+#
+
+rm tmp/*
+rm testdata/*
+rm .coveragerc.*

rapidtide/tests/test_delayestimation.py

@@ -24,8 +24,8 @@ import numpy as np
 
 import rapidtide.calcsimfunc as tide_calcsimfunc
 import rapidtide.filter as tide_filt
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.helper_classes as tide_classes
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 import rapidtide.miscmath as tide_math
 import rapidtide.peakeval as tide_peakeval
 import rapidtide.resample as tide_resample
@@ -335,7 +335,7 @@ def test_delayestimation(displayplots=False, debug=False):
         filteredwaveforms[i, :] = theprefilter.apply(Fs, waveforms[i, :])
 
     for nprocs in [4, 1]:
-        voxelsprocessed_glm = tide_glmpass.glmpass(
+        voxelsprocessed_regressionfilt = tide_linfitfiltpass.linfitfiltpass(
             numlocs,
             waveforms[:, :],
             threshval,
@@ -366,7 +366,7 @@ def test_delayestimation(displayplots=False, debug=False):
         ax.legend()
         plt.show()
 
-        print(proctype, "glmpass", np.mean(diffsignal), np.max(np.fabs(diffsignal)))
+        print(proctype, "linfitfiltpass", np.mean(diffsignal), np.max(np.fabs(diffsignal)))
 
     # clean up shared memory
     tide_util.cleanup_shm(waveforms_shm)

rapidtide/tests/test_fastresampler.py

@@ -23,8 +23,7 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 from rapidtide.resample import FastResampler, FastResamplerFromFile
-from rapidtide.tests.utils import mse
-from rapidtide.tests.utils import get_test_temp_path
+from rapidtide.tests.utils import get_test_temp_path, mse
 
 
 def test_FastResampler(debug=False):

rapidtide/tests/test_fullrunhappy_v1.py

@@ -33,7 +33,7 @@ def test_fullrunhappy_v1(debug=False, displayplots=False):
         os.path.join(get_test_temp_path(), "happyout1"),
         "--mklthreads",
         "-1",
-        "--spatialglm",
+        "--spatialregression",
         "--model",
         "model_revised",
     ]

rapidtide/tests/test_fullrunhappy_v2.py

@@ -40,7 +40,7 @@ def test_fullrunhappy_v2(debug=False, displayplots=False):
         "--model",
         "model_revised",
         "--fliparteries",
-        "--temporalglm",
+        "--temporalregression",
         "--cardiacfile",
         os.path.join(
             get_examples_path(),

rapidtide/tests/test_fullrunrapidtide_v1.py

@@ -62,7 +62,7 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--noglm",
+        "--nodenoise",
         "--norefinedelay",
         "--initialdelay",
         "0.0",
@@ -83,7 +83,7 @@ def test_fullrunrapidtide_v1(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--noglm",
+        "--nodenoise",
         "--initialdelay",
         os.path.join(get_test_temp_path(), "sub-RAPIDTIDETEST1_desc-maxtime_map.nii.gz"),
     ]

rapidtide/tests/test_fullrunrapidtide_v3.py

@@ -40,7 +40,7 @@ def test_fullrunrapidtide_v3(debug=False, displayplots=False):
         "pca",
         "--convergencethresh",
         "0.5",
-        "--noglm",
+        "--nodenoise",
         "--nprocs",
         "-1",
         "--similaritymetric",

rapidtide/tests/test_fullrunrapidtide_v5.py

@@ -35,7 +35,7 @@ def test_fullrunrapidtide_v5(debug=False, displayplots=False):
         "--passes",
         "2",
         "--numnull",
-        "0",
+        "10000",
         "--pickleft",
         "--norefinedelay",
         "--refineprenorm",

rapidtide/tests/test_fullrunrapidtide_v6.py

@@ -24,7 +24,7 @@ import matplotlib as mpl
 import rapidtide.io as tide_io
 import rapidtide.workflows.rapidtide as rapidtide_workflow
 import rapidtide.workflows.rapidtide_parser as rapidtide_parser
-import rapidtide.workflows.retroglm as rapidtide_retroglm
+import rapidtide.workflows.retroregress as rapidtide_retroregress
 from rapidtide.tests.utils import get_examples_path, get_test_temp_path
 
 
@@ -44,7 +44,7 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         "1",
         "--despecklepasses",
         "3",
-        "--glmderivs",
+        "--regressderivs",
         "0",
         "--delaypatchthresh",
         "4.0",
@@ -60,13 +60,13 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         os.path.join(get_test_temp_path(), "2deriv"),
         "--nprocs",
         "-1",
-        "--glmderivs",
+        "--regressderivs",
         "2",
         "--makepseudofile",
         "--outputlevel",
         "max",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
         os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
@@ -75,14 +75,14 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         os.path.join(get_test_temp_path(), "1deriv_refined_corrected"),
         "--nprocs",
         "1",
-        "--glmderivs",
+        "--regressderivs",
         "1",
         "--makepseudofile",
         "--outputlevel",
         "max",
         "--nofilterwithrefineddelay",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     inputargs = [
         os.path.join(get_examples_path(), "sub-RAPIDTIDETEST.nii.gz"),
@@ -91,22 +91,22 @@ def test_fullrunrapidtide_v6(debug=False, displayplots=False):
         os.path.join(get_test_temp_path(), "concordance"),
         "--nprocs",
         "-1",
-        "--glmderivs",
+        "--regressderivs",
         "0",
         "--delaypatchthresh",
         "4.0",
         "--outputlevel",
         "max",
     ]
-    rapidtide_retroglm.retroglm(rapidtide_retroglm.process_args(inputargs=inputargs))
+    rapidtide_retroregress.retroregress(rapidtide_retroregress.process_args(inputargs=inputargs))
 
     absthresh = 1e-10
     msethresh = 1e-12
     spacetolerance = 1e-3
     for map in [
-        "glmderivratios",
-        "medfiltglmderivratios",
-        "filteredglmderivratios",
+        "regressderivratios",
+        "medfiltregressderivratios",
+        "filteredregressderivratios",
         "maxtimerefined",
         "lfofilterInbandVarianceBefore",
         "lfofilterInbandVarianceAfter",

rapidtide/tests/{test_glmpass.py → test_linfitfiltpass.py}

@@ -20,7 +20,7 @@ import matplotlib as mpl
 import matplotlib.pyplot as plt
 import numpy as np
 
-import rapidtide.glmpass as tide_glmpass
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 from rapidtide.tests.utils import mse
 
 
@@ -41,7 +41,7 @@ def gen2d(xsize=150, xcycles=11, tsize=200, tcycles=13, mean=10.0):
     return thearray, xwaves, twaves
 
 
-def test_glmpass(debug=True, displayplots=False):
+def test_linfitfiltpass(debug=True, displayplots=False):
     np.random.seed(12345)
     xsize = 150
     xcycles = 7
@@ -77,8 +77,8 @@ def test_glmpass(debug=True, displayplots=False):
     fitcoffs_x = np.zeros((xsize, tsize), dtype=np.float64)
     fitNorm_x = np.zeros((xsize, tsize), dtype=np.float64)
 
-    for confoundglm in [True, False]:
-        if confoundglm:
+    for confoundregress in [True, False]:
+        if confoundregress:
             twaveformrange = np.transpose(twaveforms[:6, :])
             xwaveformrange = xwaveforms[:, :6]
             print(f"{twaveformrange.shape=} - {xwaveformrange.shape=}")
@@ -115,9 +115,9 @@ def test_glmpass(debug=True, displayplots=False):
 
                     if debug:
                         print(
-                            f"confoundglm={confoundglm}, proc by {direction}, {procstring} proc, {maskstatus}"
+                            f"confoundregress={confoundregress}, proc by {direction}, {procstring} proc, {maskstatus}"
                         )
-                    tide_glmpass.glmpass(
+                    tide_linfitfiltpass.linfitfiltpass(
                         xsize,
                         testarray,
                         thisthreshval,
@@ -132,7 +132,7 @@ def test_glmpass(debug=True, displayplots=False):
                         showprogressbar=False,
                         procbyvoxel=procbyvoxel,
                         nprocs=nprocs,
-                        confoundglm=confoundglm,
+                        confoundregress=confoundregress,
                     )
                     if displayplots:
                         plt.figure()
@@ -142,10 +142,10 @@ def test_glmpass(debug=True, displayplots=False):
                         plt.show()
                     if debug:
                         print(f"\tMSE: {mse(datatoremove, targetarray)}\n")
-                    if not confoundglm:
+                    if not confoundregress:
                         assert mse(datatoremove, targetarray) < 1e-3
 
 
 if __name__ == "__main__":
     mpl.use("TkAgg")
-    test_glmpass(debug=True, displayplots=True)
+    test_linfitfiltpass(debug=True, displayplots=True)

rapidtide/tests/test_motionregress.py

@@ -21,8 +21,8 @@ import matplotlib.pyplot as plt
 import numpy as np
 
 import rapidtide.fit as tide_fit
-import rapidtide.glmpass as tide_glmpass
 import rapidtide.io as tide_io
+import rapidtide.linfitfiltpass as tide_linfitfiltpass
 from rapidtide.tests.utils import mse
 
 
@@ -132,7 +132,7 @@ def test_motionregress(debug=False, displayplots=False):
                 numprocitems = thedataarray.shape[0]
                 filtereddata = thedataarray * 0.0
                 r2value = np.zeros(numprocitems)
-                dummy = tide_glmpass.glmpass(
+                dummy = tide_linfitfiltpass.linfitfiltpass(
                     numprocitems,
                     thedataarray,
                     None,
@@ -144,7 +144,7 @@ def test_motionregress(debug=False, displayplots=False):
                     None,
                     None,
                     filtereddata,
-                    confoundglm=True,
+                    confoundregress=True,
                     nprocs=1,
                     showprogressbar=debug,
                     procbyvoxel=True,

rapidtide/tests/test_refinedelay.py

@@ -80,7 +80,7 @@ def eval_refinedelay(
     padtime = sampletime * numpadtrs
     lagtcgenerator = tide_resample.FastResampler(timeaxis, sLFO, padtime=padtime)
 
-    # find the mapping of glm ratios to delays
+    # find the mapping of derivative ratios to delays
     tide_refinedelay.trainratiotooffset(
         lagtcgenerator,
         timeaxis,
@@ -135,7 +135,7 @@ def eval_refinedelay(
 
     rt_floattype = "float64"
     rt_floatset = np.float64
-    glmmean = np.zeros(numlags, dtype=rt_floattype)
+    sLFOfitmean = np.zeros(numlags, dtype=rt_floattype)
     rvalue = np.zeros(numlags, dtype=rt_floattype)
     r2value = np.zeros(numlags, dtype=rt_floattype)
     fitNorm = np.zeros((numlags, 2), dtype=rt_floattype)
@@ -144,10 +144,10 @@ def eval_refinedelay(
     lagtc = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
     filtereddata = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
     optiondict = {
-        "glmthreshval": 0.0,
-        "saveminimumglmfiles": False,
+        "regressfiltthreshval": 0.0,
+        "saveminimumsLFOfiltfiles": False,
         "nprocs_makelaggedtcs": 1,
-        "nprocs_glm": 1,
+        "nprocs_regressionfilt": 1,
         "mp_chunksize": 1000,
         "showprogressbar": False,
         "alwaysmultiproc": False,
@@ -157,7 +157,7 @@ def eval_refinedelay(
         "textio": False,
     }
 
-    glmderivratios = tide_refinedelay.getderivratios(
+    regressderivratios, regressrvalues = tide_refinedelay.getderivratios(
         fmridata,
         validvoxels,
         timeaxis,
@@ -167,7 +167,7 @@ def eval_refinedelay(
         "glm",
         "refinedelaytest",
         sampletime,
-        glmmean,
+        sLFOfitmean,
         rvalue,
         r2value,
         fitNorm[:, :2],
@@ -181,8 +181,8 @@ def eval_refinedelay(
         debug=debug,
     )
 
-    medfilt, filteredglmderivratios, themad = tide_refinedelay.filterderivratios(
-        glmderivratios,
+    medfilt, filteredregressderivratios, themad = tide_refinedelay.filterderivratios(
+        regressderivratios,
         nativespaceshape,
         validvoxels,
         (xdim, ydim, slicedim),
@@ -193,9 +193,9 @@ def eval_refinedelay(
         debug=debug,
     )
 
-    delayoffset = filteredglmderivratios * 0.0
-    for i in range(filteredglmderivratios.shape[0]):
-        delayoffset[i] = tide_refinedelay.ratiotodelay(filteredglmderivratios[i])
+    delayoffset = filteredregressderivratios * 0.0
+    for i in range(filteredregressderivratios.shape[0]):
+        delayoffset[i] = tide_refinedelay.ratiotodelay(filteredregressderivratios[i])
 
     # do the tests
     msethresh = 0.1