rapidtide 2.9.5__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide/calcandfitcorrpairs.py

@@ -1,262 +0,0 @@
-#!/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 gc
-import logging
-import warnings
-
-import numpy as np
-from tqdm import tqdm
-
-import rapidtide.correlate as tide_corr
-import rapidtide.fit as tide_fit
-import rapidtide.multiproc as tide_multiproc
-
-warnings.simplefilter(action="ignore", category=FutureWarning)
-LGR = logging.getLogger("GENERAL")
-
-
-def _procOneVoxelCorrelation(
-    thedata,
-    index,
-    neighborindex,
-    Fs,
-    dofit=False,
-    lagmin=-12.5,
-    lagmax=12.5,
-    widthmax=100.0,
-    negsearch=15.0,
-    possearch=15.0,
-    padding=0,
-    debug=False,
-):
-    tc1 = thedata[index, :]
-    tc2 = thedata[neighborindex, :]
-    if np.any(tc1) != 0.0 and np.any(tc2) != 0.0:
-        thesimfunc = tide_corr.fastcorrelate(
-            tc1,
-            tc2,
-            zeropadding=padding,
-            usefft=True,
-            debug=debug,
-        )
-        similarityfunclen = len(thesimfunc)
-        similarityfuncorigin = similarityfunclen // 2 + 1
-
-        negpoints = int(negsearch * Fs)
-        pospoints = int(possearch * Fs)
-        trimsimfunc = thesimfunc[
-            similarityfuncorigin - negpoints : similarityfuncorigin + pospoints
-        ]
-        offset = 0.0
-        trimtimeaxis = (
-            (
-                np.arange(0.0, similarityfunclen) * (1.0 / Fs)
-                - ((similarityfunclen - 1) * (1.0 / Fs)) / 2.0
-            )
-            - offset
-        )[similarityfuncorigin - negpoints : similarityfuncorigin + pospoints]
-        if dofit:
-            (
-                maxindex,
-                maxtime,
-                maxcorr,
-                maxsigma,
-                maskval,
-                failreason,
-                peakstart,
-                peakend,
-            ) = tide_fit.simfuncpeakfit(
-                trimsimfunc,
-                trimtimeaxis,
-                useguess=False,
-                maxguess=0.0,
-                displayplots=False,
-                functype="correlation",
-                peakfittype="gauss",
-                searchfrac=0.5,
-                lagmod=1000.0,
-                enforcethresh=True,
-                allowhighfitamps=False,
-                lagmin=lagmin,
-                lagmax=lagmax,
-                absmaxsigma=1000.0,
-                absminsigma=0.25,
-                hardlimit=True,
-                bipolar=False,
-                lthreshval=0.0,
-                uthreshval=1.0,
-                zerooutbadfit=True,
-                debug=False,
-            )
-        else:
-            maxtime = trimtimeaxis[np.argmax(trimsimfunc)]
-            maxcorr = np.max(trimsimfunc)
-            maskval = 1
-            failreason = 0
-        if debug:
-            print(f"{maxtime=}")
-            print(f"{maxcorr=}")
-            print(f"{maskval=}")
-            print(f"{negsearch=}")
-            print(f"{possearch=}")
-            print(f"{Fs=}")
-            print(f"{len(trimtimeaxis)=}")
-            print(trimsimfunc, trimtimeaxis)
-        return index, neighborindex, maxcorr, maxtime, maskval, failreason
-    else:
-        return index, neighborindex, 0.0, 0.0, 0, 0
-
-
-def correlationpass(
-    fmridata,
-    referencetc,
-    theCorrelator,
-    fmri_x,
-    os_fmri_x,
-    lagmininpts,
-    lagmaxinpts,
-    corrout,
-    meanval,
-    nprocs=1,
-    alwaysmultiproc=False,
-    oversampfactor=1,
-    interptype="univariate",
-    showprogressbar=True,
-    chunksize=1000,
-    rt_floatset=np.float64,
-    rt_floattype="float64",
-):
-    """
-
-    Parameters
-    ----------
-    fmridata
-    referencetc - the reference regressor, already oversampled
-    theCorrelator
-    fmri_x
-    os_fmri_x
-    tr
-    lagmininpts
-    lagmaxinpts
-    corrout
-    meanval
-    nprocs
-    oversampfactor
-    interptype
-    showprogressbar
-    chunksize
-    rt_floatset
-    rt_floattype
-
-    Returns
-    -------
-
-    """
-    inputshape = np.shape(fmridata)
-    volumetotal = 0
-    thetc = np.zeros(np.shape(os_fmri_x), dtype=rt_floattype)
-    theglobalmaxlist = []
-    if nprocs > 1 or alwaysmultiproc:
-        # define the consumer function here so it inherits most of the arguments
-        def correlation_consumer(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(
-                        _procOneVoxelCorrelation(
-                            val,
-                            idx1,
-                            idx2,
-                            Fs,
-                            dofit=False,
-                            lagmin=-12.5,
-                            lagmax=12.5,
-                            widthmax=100.0,
-                            negsearch=15.0,
-                            possearch=15.0,
-                            padding=0,
-                            debug=False,
-                        )
-                    )
-
-                except Exception as e:
-                    print("error!", e)
-                    break
-
-        data_out = tide_multiproc.run_multiproc(
-            correlation_consumer,
-            inputshape,
-            None,
-            nprocs=nprocs,
-            showprogressbar=showprogressbar,
-            chunksize=chunksize,
-        )
-
-        # unpack the data
-        volumetotal = 0
-        for voxel in data_out:
-            maxcorr[voxel[0], voxel[1]] = voxel[2]
-            maxtime[voxel[0], voxel[1]] = voxel[3]
-            maskval[voxel[0], voxel[1]] = voxel[4]
-            failreason[voxel[0], voxel[1]] = voxel[5]
-            volumetotal += 1
-        del data_out
-    else:
-        for vox in tqdm(
-            range(0, inputshape[0]),
-            desc="Voxel",
-            disable=(not showprogressbar),
-        ):
-            (
-                dummy,
-                meanval[vox],
-                corrout[vox, :],
-                thecorrscale,
-                theglobalmax,
-            ) = _procOneVoxelCorrelation(
-                vox,
-                thetc,
-                theCorrelator,
-                fmri_x,
-                fmridata[vox, :],
-                os_fmri_x,
-                oversampfactor=oversampfactor,
-                interptype=interptype,
-                rt_floatset=rt_floatset,
-                rt_floattype=rt_floattype,
-            )
-            theglobalmaxlist.append(theglobalmax + 0)
-            volumetotal += 1
-    LGR.info(f"\nSimilarity function calculated on {volumetotal} voxels")
-
-    # garbage collect
-    uncollected = gc.collect()
-    if uncollected != 0:
-        LGR.info(f"garbage collected - unable to collect {uncollected} objects")
-    else:
-        LGR.info("garbage collected")
-
-    return volumetotal, theglobalmaxlist, thecorrscale

rapidtide/data/examples/src/testoutputsize

@@ -1,45 +0,0 @@
-#!/bin/bash
-
-
-for LEVEL in min less normal more max
-do
-    mkdir -p ../dst/nomotregress/${LEVEL}
-    sbatch --mem=64G --time=90 --cpus-per-task 4 /cm/shared/miniforge3/envs/mic/bin/rapidtide \
-        --nprocs 4 \
-        --passes 3 \
-        --outputlevel ${LEVEL} \
-        --searchrange -5 10 \
-        --noglm \
-        /data2/HCP1200/100307/preproc/100307/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz \
-        /home/frederic/code/rapidtide/rapidtide/data/examples/dst/nomotregress/${LEVEL}/sub-RAPIDTIDETEST
-done
-
-for LEVEL in min less normal more max
-do
-    mkdir -p ../dst/motregress/${LEVEL}
-    sbatch --mem=64G --time=90 --cpus-per-task 4 /cm/shared/miniforge3/envs/mic/bin/rapidtide \
-        --nprocs 4 \
-        --passes 3 \
-        --outputlevel ${LEVEL} \
-        --searchrange -5 10 \
-        --noglm \
-        --motionfile /data2/HCP1200/100307/preproc/100307/MNINonLinear/Results/rfMRI_REST1_LR/Movement_Regressors.txt:0-5 \
-        /data2/HCP1200/100307/preproc/100307/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz \
-        /home/frederic/code/rapidtide/rapidtide/data/examples/dst/motregress/${LEVEL}/sub-RAPIDTIDETEST
-done
-
-for LEVEL in min less normal more max
-do
-    for NDERIVS in 0 1
-    do
-        mkdir -p ../dst/nomotregress/${LEVEL}glm${NDERIVS}
-        sbatch --mem=64G --time=90 --cpus-per-task 4 /cm/shared/miniforge3/envs/mic/bin/rapidtide \
-            --nprocs 4 \
-            --passes 3 \
-            --outputlevel ${LEVEL} \
-            --glmderivs ${NDERIVS} \
-            --searchrange -5 10 \
-            /data2/HCP1200/100307/preproc/100307/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR.nii.gz \
-            /home/frederic/code/rapidtide/rapidtide/data/examples/dst/nomotregress/${LEVEL}glm${NDERIVS}/sub-RAPIDTIDETEST
-    done
-done