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

rapidtide/workflows/glmfrommaps.py

@@ -1,202 +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 numpy as np
-
-import rapidtide.glmpass as tide_glmpass
-import rapidtide.io as tide_io
-import rapidtide.makelaggedtcs as tide_makelagged
-import rapidtide.miscmath as tide_math
-import rapidtide.util as tide_util
-
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
-
-def conditionalprofile():
-    def resdec(f):
-        if memprofilerexists:
-            return profile(f)
-        return f
-
-    return resdec
-
-
-@conditionalprofile()
-def memcheckpoint(message):
-    pass
-
-
-def addmemprofiling(thefunc, memprofile, themessage):
-    if memprofile:
-        return profile(thefunc, precision=2)
-    else:
-        tide_util.logmem(themessage)
-        return thefunc
-
-
-def glmfrommaps(
-    fmri_data_valid,
-    validvoxels,
-    initial_fmri_x,
-    lagtimes,
-    fitmask,
-    genlagtc,
-    mode,
-    outputname,
-    oversamptr,
-    glmmean,
-    rvalue,
-    r2value,
-    fitNorm,
-    fitcoeff,
-    movingsignal,
-    lagtc,
-    filtereddata,
-    LGR,
-    TimingLGR,
-    glmthreshval,
-    saveminimumglmfiles,
-    nprocs_makelaggedtcs=1,
-    nprocs_glm=1,
-    glmderivs=0,
-    mp_chunksize=50000,
-    showprogressbar=True,
-    alwaysmultiproc=False,
-    memprofile=False,
-    debug=False,
-):
-    if debug:
-        print("GLMFROMMAPS: Starting")
-        print(f"{nprocs_makelaggedtcs=}")
-        print(f"{nprocs_glm=}")
-        print(f"{glmderivs=}")
-        print(f"{mp_chunksize=}")
-        print(f"{showprogressbar=}")
-        print(f"{alwaysmultiproc=}")
-        print(f"{memprofile=}")
-        print(f"{mode=}")
-        print(f"{outputname=}")
-        print(f"{oversamptr=}")
-        print(f"{glmthreshval=}")
-    rt_floatset = np.float64
-    rt_floattype = "float64"
-    numvalidspatiallocs = np.shape(validvoxels)[0]
-
-    # generate the voxel specific regressors
-    LGR.info("Start lagged timecourse creation")
-    TimingLGR.info("Start lagged timecourse creation")
-    if memprofile:
-        makelagged_func = addmemprofiling(
-            tide_makelagged.makelaggedtcs,
-            memprofile,
-            "before making lagged timecourses",
-        )
-    else:
-        makelagged_func = tide_makelagged.makelaggedtcs
-    voxelsprocessed_makelagged = makelagged_func(
-        genlagtc,
-        initial_fmri_x,
-        fitmask,
-        lagtimes,
-        lagtc,
-        nprocs=nprocs_makelaggedtcs,
-        alwaysmultiproc=alwaysmultiproc,
-        showprogressbar=showprogressbar,
-        chunksize=mp_chunksize,
-        rt_floatset=rt_floatset,
-        rt_floattype=rt_floattype,
-    )
-    if debug:
-        print(f"{lagtimes.shape=}")
-        threshmask = np.where(fitmask > 0, 1, 0)
-        print(f"{np.sum(threshmask)} nonzero mask voxels")
-        print(f"after makelaggedtcs: shifted {voxelsprocessed_makelagged} timecourses")
-    LGR.info("End lagged timecourse creation")
-    TimingLGR.info(
-        "Lagged timecourse creation end",
-        {
-            "message2": voxelsprocessed_makelagged,
-            "message3": "voxels",
-        },
-    )
-
-    # and do the filtering
-    LGR.info("Start filtering operation")
-    TimingLGR.info("Start filtering operation")
-    if memprofile:
-        glmpass_func = addmemprofiling(tide_glmpass.glmpass, memprofile, "before glmpass")
-    else:
-        glmpass_func = tide_glmpass.glmpass
-
-    if glmderivs > 0:
-        if debug:
-            print(f"adding derivatives up to order {glmderivs} prior to regression")
-        regressorset = tide_glmpass.makevoxelspecificderivs(lagtc, glmderivs)
-    else:
-        if debug:
-            print(f"using raw lagged regressors for regression")
-        regressorset = lagtc
-    if debug:
-        print(f"{regressorset.shape=}")
-    voxelsprocessed_glm = glmpass_func(
-        numvalidspatiallocs,
-        fmri_data_valid,
-        glmthreshval,
-        regressorset,
-        glmmean,
-        rvalue,
-        r2value,
-        fitcoeff,
-        fitNorm,
-        movingsignal,
-        filtereddata,
-        nprocs=nprocs_glm,
-        alwaysmultiproc=alwaysmultiproc,
-        showprogressbar=showprogressbar,
-        mp_chunksize=mp_chunksize,
-        rt_floatset=rt_floatset,
-        rt_floattype=rt_floattype,
-    )
-
-    if mode == "cvrmap":
-        # if we are doing a cvr map, multiply the fitcoeff by 100, so we are in percent
-        fitcoeff *= 100.0
-
-    # determine what was removed
-    removeddata = fmri_data_valid - filtereddata
-    noiseremoved = np.var(removeddata, axis=0)
-    if saveminimumglmfiles:
-        tide_io.writebidstsv(
-            f"{outputname}_desc-lfofilterNoiseRemoved_timeseries",
-            noiseremoved,
-            1.0 / oversamptr,
-            starttime=0.0,
-            columns=[f"removedbyglm"],
-            extraheaderinfo={
-                "Description": "Variance over space of data removed by GLM filter at each timepoint"
-            },
-            append=False,
-        )
-
-    return voxelsprocessed_glm, regressorset