rapidtide 3.0.5__py3-none-any.whl → 3.0.7__py3-none-any.whl

rapidtide/data/examples/src/testatlasaverage

@@ -21,3 +21,25 @@ atlasaverage \
     --extramask /opt/fsl-latest/data/standard/MNI152_T1_1mm_brain_mask.nii.gz \
     --summarymethod median \
     --headerline
+
+atlasaverage \
+    sub-RAPIDTIDETEST.nii.gz \
+    sub-RAPIDTIDETEST_dseg.nii.gz \
+    ../dst/synthsegaverages \
+    --ignorezeros \
+    --numpercentiles 3 \
+    --includemask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --regionlabelfile dseglabels.txt \
+    --summarymethod mean 
+
+atlasaverage \
+    sub-RAPIDTIDETEST.nii.gz \
+    sub-RAPIDTIDETEST_dseg.nii.gz \
+    ../dst/synthsegaverages_pctnorm \
+    --normmethod pct \
+    --ignorezeros \
+    --numpercentiles 3 \
+    --includemask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --regionlabelfile dseglabels.txt \
+    --summarymethod mean 
+

rapidtide/data/examples/src/testfmri

@@ -6,10 +6,25 @@ rapidtide \
     --searchrange -5 20 \
     --simcalcrange 50 -1 \
     --outputlevel more \
-    --dofinalrefine \
     --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
     --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
     --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    --cleanrefined \
     sub-RAPIDTIDETEST.nii.gz \
     ../dst/sub-RAPIDTIDETEST
+
+rapidtide \
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nosLFOfiltmask \
+    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+    --cleanrefined \
+    sub-RAPIDTIDETEST.nii.gz \
+    ../dst/sub-RAPIDTIDETEST_nosLFOfiltmask

rapidtide/data/examples/src/testhappy

@@ -1,80 +1,77 @@
 #!/bin/csh -f
 
 #happy \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/100206_3T_rfMRI_REST1_LR.nii.gz \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/rfMRI_REST1_LR/slicetimes.txt \
-#    ~/Dropbox_PHC/MR_data_2/physioconn/happytest/happyarm \
-#    --mklthreads -1 \
-#    --infotag tag1 value1 \
-#    --infotag tag2 value2 \
-#    --model model_revised
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    ../dst/happy_vanilla \
+#    --nprocs 1
 
 #happy \
-    #sub-HAPPYTEST.nii.gz \
-    #sub-HAPPYTEST.json \
-    #../dst/happy \
-    #--mklthreads 8 \
-    #--model model_revised \
-    #--spatialglm --aliasedcorrelation
-
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --mpphaseproject \
+#    ../dst/happy_mpphaseproj \
+#    --nprocs -1
 
 #happy \
 #    sub-HAPPYTEST.nii.gz \
 #    sub-HAPPYTEST.json \
-#    ../dst/happy_2comp \
-#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
-#    --mklthreads 8 \
-#    --hilbertcomponents 2 \
-#    --model model_revised
-#
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend \
+#    --nprocs -1
+
 #happy \
 #    sub-HAPPYTEST.nii.gz \
 #    sub-HAPPYTEST.json \
-#    ../dst/happy_3comp \
-#    --cardiacfile happystdres_bids.tsv:normcardiac_25.0Hz \
-#    --mklthreads 8 \
-#    --hilbertcomponents 3 \
-#    --model model_revised
+#    --mpphaseproject \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_mpphaseproj \
+#    --nprocs -1
 
-#happy_legacy \
-    #sub-HAPPYTEST.nii.gz \
-    #sub-HAPPYTEST.json \
-    #../dst/happy_normaltest \
-    #--mklthreads=8 \
-    #--model=model_revised \
-    #--outputbins=40 \
-    #--gridbins=3.5 \
-    #--stdfreq=20.0 \
-    #--estmask=happytestvesselmask.nii.gz \
-    #--minhr=46 \
-    #--maxhr=131.2 \
-    #--minhrfilt=45.5 \
-    #--maxhrfilt=800.0 \
-    #--envcutoff=0.45 \
-    #--notchwidth=1.25 \
-    #--cardiacfile=happytestpleth.txt \
-    #--cardiacfreq=20.0 \
-    #--cardiacstart=0.0 \
-    #--aliasedcorrelation \
-    #--increaseoutputlevel \
-    #--increaseoutputlevel \
-    #--decreaseoutputlevel \
-    #--dodlfilter
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    ../dst/happy_vanilla_prefill \
+#    --nprocs 1
 
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpphaseproject \
+#    ../dst/happy_mpphaseproj_prefill \
+#    --nprocs -1
 
-happy \
-    sub-HAPPYTEST.nii.gz \
-    sub-HAPPYTEST.json \
-    ../dst/happy
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_prefill \
+#    --nprocs -1
 
-happy \
-    sub-HAPPYTEST.nii.gz \
-    sub-HAPPYTEST.json \
-    --model ~/code/rapidtide/rapidtide/data/models/model_cnn_w064_l13_fn20_fl08 \
-    ../dst/happy_newcnn
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    --prefillcongrid \
+#    --mpphaseproject \
+#    --mpdetrend \
+#    ../dst/happy_mpdetrend_mpphaseproj_prefill \
+#    --nprocs -1
 
 #happy \
     #sub-HAPPYTEST.nii.gz \
     #sub-HAPPYTEST.json \
-    #../dst/happy
-#
+    #--mpphaseproject \
+    #--mpdetrend \
+    #--nocongridcache \
+    #../dst/happy_mpdetrend_mpphaseproj_nocache \
+    #--nprocs -1
+
+happy \
+    sub-HAPPYTEST.nii.gz \
+    sub-HAPPYTEST.json \
+    ../dst/happy_newdefaults \
+    --aliasedcorrelation \
+    --nprocs -1

rapidtide/data/examples/src/testsimdata

@@ -1,36 +1,53 @@
 #!/bin/bash
 
+#rapidtide \
+#    --spatialfilt -1 \
+#    --nprocs -1 \
+#    --searchrange -5 20 \
+#    --simcalcrange 50 -1 \
+#    --outputlevel more \
+#    --nofitfilt \
+#    --corrtype linear \
+#    sub-RAPIDTIDETEST.nii.gz \
+#    ../dst/sub-RAPIDTIDETEST
+
+simdata \
+    1.5 \
+    260 \
+    ../dst/sub-RAPIDTIDETEST_desc-unfiltmean_map.nii.gz \
+    ../dst/simulatedfmri_vn05 \
+    --lfopctfile ../dst/sub-RAPIDTIDETEST_desc-maxcorr_map.nii.gz \
+    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtimerefined_map.nii.gz \
+    --lforegressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 \
+    --voxelnoiselevel 5.0
+
 rapidtide \
-	--spatialfilt 2 \
-        --nprocs -1 \
-        --passes 3 \
-        --nofitfilt \
-        --similaritymetric hybrid \
-        --norefinedespeckled \
-        --filterband lfo \
-        --corrtype linear \
-        sub-RAPIDTIDETEST.nii.gz \
-        ../dst/sub-RAPIDTIDETEST
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_vn05.nii.gz \
+    ../dst/simrapidtide_vn05
 
 simdata \
-    sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_desc-mean_map.nii.gz \
-    ../dst/simulatedfmri \
-    sub-RAPIDTIDETEST.json \
-    --lfopctfile ../dst/sub-RAPIDTIDETEST_desc-corrfit_mask.nii.gz \
-    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtime_map.nii.gz \
+    1.5 \
+    260 \
+    ../dst/sub-RAPIDTIDETEST_desc-unfiltmean_map.nii.gz \
+    ../dst/simulatedfmri_sigfrac \
+    --lfosignalfraction ../dst/sub-RAPIDTIDETEST_desc-lfofilterInbandVarianceChange_map.nii.gz \
+    --lfolagfile ../dst/sub-RAPIDTIDETEST_desc-maxtimerefined_map.nii.gz \
     --lforegressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 
 
 rapidtide \
-        --spatialfilt 2 \
-        --nprocs -1 \
-        --passes 3 \
-        --nofitfilt \
-        --similaritymetric hybrid \
-        --regressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 \
-        --CVR \
-        --filterband lfo \
-        --corrtype linear \
-        ../dst/simulatedfmri.nii.gz \
-        ../dst/simrapidtide
-
+    --spatialfilt -1 \
+    --nprocs -1 \
+    --searchrange -5 20 \
+    --simcalcrange 50 -1 \
+    --outputlevel more \
+    --nofitfilt \
+    --corrtype linear \
+    ../dst/simulatedfmri_sigfrac.nii.gz \
+    ../dst/simrapidtide_sigfrac

rapidtide/genericmultiproc.py

@@ -0,0 +1,122 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+#   Copyright 2016-2025 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 gc
+import logging
+
+import numpy as np
+from tqdm import tqdm
+
+import rapidtide.multiproc as tide_multiproc
+
+
+def run_multiproc(
+    voxelfunc,
+    packfunc,
+    unpackfunc,
+    voxelargs,
+    voxelproducts,
+    inputshape,
+    voxelmask,
+    LGR,
+    nprocs,
+    alwaysmultiproc,
+    showprogressbar,
+    chunksize,
+    indexaxis=0,
+    procunit="voxels",
+    debug=False,
+    **kwargs,
+):
+    if debug:
+        print(f"{len(voxelproducts)=}, {voxelproducts[0].shape}")
+    if nprocs > 1 or alwaysmultiproc:
+        # define the consumer function here so it inherits most of the arguments
+        def theconsumerfunc(inQ, outQ):
+            while True:
+                try:
+                    # get a new message
+                    val = inQ.get()
+
+                    # this is the 'TERM' signal
+                    if val is None:
+                        break
+
+                    # process and send the data
+                    outQ.put(
+                        voxelfunc(
+                            val,
+                            packfunc(val, voxelargs),
+                            debug=debug,
+                            **kwargs,
+                        )
+                    )
+                except Exception as e:
+                    print("error!", e)
+                    break
+
+        data_out = tide_multiproc.run_multiproc(
+            theconsumerfunc,
+            inputshape,
+            voxelmask,
+            indexaxis=indexaxis,
+            procunit=procunit,
+            verbose=(LGR is not None),
+            nprocs=nprocs,
+            showprogressbar=showprogressbar,
+            chunksize=chunksize,
+        )
+
+        # unpack the data
+        volumetotal = 0
+        for returnvals in data_out:
+            volumetotal += 1
+            unpackfunc(returnvals, voxelproducts)
+        del data_out
+    else:
+        volumetotal = 0
+        for vox in tqdm(
+            range(0, inputshape[indexaxis]),
+            desc="Voxel",
+            unit=procunit,
+            disable=(not showprogressbar),
+        ):
+            if voxelmask[vox] > 0:
+                dothisone = True
+            else:
+                dothisone = False
+            if dothisone:
+                returnvals = voxelfunc(
+                    vox,
+                    packfunc(vox, voxelargs),
+                    debug=debug,
+                    **kwargs,
+                )
+                unpackfunc(returnvals, voxelproducts)
+                volumetotal += 1
+
+    # garbage collect
+    uncollected = gc.collect()
+    if uncollected != 0:
+        if LGR is not None:
+            LGR.info(f"garbage collected - unable to collect {uncollected} objects")
+    else:
+        if LGR is not None:
+            LGR.info("garbage collected")
+
+    return volumetotal