rapidtide 3.0a14__py3-none-any.whl → 3.0a15__py3-none-any.whl

rapidtide/workflows/delayestimation.py

@@ -0,0 +1,488 @@
+#!/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 argparse
+import sys
+
+import numpy as np
+from scipy.stats import skew
+
+import rapidtide.io as tide_io
+import rapidtide.workflows.parser_funcs as pf
+
+try:
+    import mkl
+
+    mklexists = True
+except ImportError:
+    mklexists = False
+
+
+def disablemkl(numprocs, debug=False):
+    if mklexists:
+        if numprocs > 1:
+            if debug:
+                print("disablemkl: setting threads to 1")
+            mkl.set_num_threads(1)
+
+
+def enablemkl(numthreads, debug=False):
+    if mklexists:
+        if debug:
+            print(f"enablemkl: setting threads to {numthreads}")
+        mkl.set_num_threads(numthreads)
+
+
+def estimateDelay(voxeldata, datatimeaxis, osdatatimeaxis, theMutualInformationator, thepass):
+    # Step 1 - Correlation step
+    if optiondict["similaritymetric"] == "mutualinfo":
+        similaritytype = "Mutual information"
+    elif optiondict["similaritymetric"] == "correlation":
+        similaritytype = "Correlation"
+    else:
+        similaritytype = "MI enhanced correlation"
+    LGR.info(f"\n\n{similaritytype} calculation, pass {thepass}")
+    TimingLGR.info(f"{similaritytype} calculation start, pass {thepass}")
+
+    disablemkl(optiondict["nprocs_calcsimilarity"], debug=threaddebug)
+    if optiondict["similaritymetric"] == "mutualinfo":
+        theMutualInformationator.setlimits(lagmininpts, lagmaxinpts)
+        (
+            voxelsprocessed_cp,
+            theglobalmaxlist,
+            trimmedcorrscale,
+        ) = tide_calcsimfunc.correlationpass(
+            voxeldata,
+            cleaned_referencetc,
+            theMutualInformationator,
+            datatimeaxis,
+            osdatatimeaxis,
+            lagmininpts,
+            lagmaxinpts,
+            corrout,
+            meanval,
+            nprocs=optiondict["nprocs_calcsimilarity"],
+            alwaysmultiproc=optiondict["alwaysmultiproc"],
+            oversampfactor=optiondict["oversampfactor"],
+            interptype=optiondict["interptype"],
+            showprogressbar=optiondict["showprogressbar"],
+            chunksize=optiondict["mp_chunksize"],
+            rt_floatset=rt_floatset,
+            rt_floattype=rt_floattype,
+        )
+    else:
+        (
+            voxelsprocessed_cp,
+            theglobalmaxlist,
+            trimmedcorrscale,
+        ) = tide_calcsimfunc.correlationpass(
+            voxeldata,
+            cleaned_referencetc,
+            theCorrelator,
+            datatimeaxis,
+            osdatatimeaxis,
+            lagmininpts,
+            lagmaxinpts,
+            corrout,
+            meanval,
+            nprocs=optiondict["nprocs_calcsimilarity"],
+            alwaysmultiproc=optiondict["alwaysmultiproc"],
+            oversampfactor=optiondict["oversampfactor"],
+            interptype=optiondict["interptype"],
+            showprogressbar=optiondict["showprogressbar"],
+            chunksize=optiondict["mp_chunksize"],
+            rt_floatset=rt_floatset,
+            rt_floattype=rt_floattype,
+        )
+    enablemkl(optiondict["mklthreads"], debug=threaddebug)
+
+    for i in range(len(theglobalmaxlist)):
+        theglobalmaxlist[i] = corrscale[theglobalmaxlist[i]] - optiondict["simcalcoffset"]
+    namesuffix = "_desc-globallag_hist"
+    tide_stats.makeandsavehistogram(
+        np.asarray(theglobalmaxlist),
+        len(corrscale),
+        0,
+        outputname + namesuffix,
+        displaytitle="Histogram of lag times from global lag calculation",
+        therange=(corrscale[0], corrscale[-1]),
+        refine=False,
+        dictvarname="globallaghist_pass" + str(thepass),
+        append=(optiondict["echocancel"] or (thepass > 1)),
+        thedict=optiondict,
+    )
+
+    if optiondict["checkpoint"]:
+        outcorrarray[:, :] = 0.0
+        outcorrarray[validvoxels, :] = corrout[:, :]
+        if optiondict["textio"]:
+            tide_io.writenpvecs(
+                outcorrarray.reshape(nativecorrshape),
+                f"{outputname}_corrout_prefit_pass" + str(thepass) + ".txt",
+            )
+        else:
+            savename = f"{outputname}_desc-corroutprefit_pass-" + str(thepass)
+            tide_io.savetonifti(outcorrarray.reshape(nativecorrshape), theheader, savename)
+
+    TimingLGR.info(
+        f"{similaritytype} calculation end, pass {thepass}",
+        {
+            "message2": voxelsprocessed_cp,
+            "message3": "voxels",
+        },
+    )
+
+    # Step 1b.  Do a peak prefit
+    if optiondict["similaritymetric"] == "hybrid":
+        LGR.info(f"\n\nPeak prefit calculation, pass {thepass}")
+        TimingLGR.info(f"Peak prefit calculation start, pass {thepass}")
+
+        disablemkl(optiondict["nprocs_peakeval"], debug=threaddebug)
+        voxelsprocessed_pe, thepeakdict = tide_peakeval.peakevalpass(
+            voxeldata,
+            cleaned_referencetc,
+            datatimeaxis,
+            osdatatimeaxis,
+            theMutualInformationator,
+            trimmedcorrscale,
+            corrout,
+            nprocs=optiondict["nprocs_peakeval"],
+            alwaysmultiproc=optiondict["alwaysmultiproc"],
+            bipolar=optiondict["bipolar"],
+            oversampfactor=optiondict["oversampfactor"],
+            interptype=optiondict["interptype"],
+            showprogressbar=optiondict["showprogressbar"],
+            chunksize=optiondict["mp_chunksize"],
+            rt_floatset=rt_floatset,
+            rt_floattype=rt_floattype,
+        )
+        enablemkl(optiondict["mklthreads"], debug=threaddebug)
+
+        TimingLGR.info(
+            f"Peak prefit end, pass {thepass}",
+            {
+                "message2": voxelsprocessed_pe,
+                "message3": "voxels",
+            },
+        )
+        mipeaks = lagtimes * 0.0
+        for i in range(numvalidspatiallocs):
+            if len(thepeakdict[str(i)]) > 0:
+                mipeaks[i] = thepeakdict[str(i)][0][0]
+    else:
+        thepeakdict = None
+
+    # Step 2 - similarity function fitting and time lag estimation
+    # write out the current version of the run options
+    optiondict["currentstage"] = f"presimfuncfit_pass{thepass}"
+    tide_io.writedicttojson(optiondict, f"{outputname}_desc-runoptions_info.json")
+    LGR.info(f"\n\nTime lag estimation pass {thepass}")
+    TimingLGR.info(f"Time lag estimation start, pass {thepass}")
+
+    theFitter.setfunctype(optiondict["similaritymetric"])
+    theFitter.setcorrtimeaxis(trimmedcorrscale)
+
+    # use initial lags if this is a hybrid fit
+    if optiondict["similaritymetric"] == "hybrid" and thepeakdict is not None:
+        initlags = mipeaks
+    else:
+        initlags = None
+
+    disablemkl(optiondict["nprocs_fitcorr"], debug=threaddebug)
+    voxelsprocessed_fc = tide_simfuncfit.fitcorr(
+        trimmedcorrscale,
+        theFitter,
+        corrout,
+        fitmask,
+        failreason,
+        lagtimes,
+        lagstrengths,
+        lagsigma,
+        gaussout,
+        windowout,
+        R2,
+        despeckling=False,
+        peakdict=thepeakdict,
+        nprocs=optiondict["nprocs_fitcorr"],
+        alwaysmultiproc=optiondict["alwaysmultiproc"],
+        fixdelay=optiondict["fixdelay"],
+        initialdelayvalue=theinitialdelay,
+        showprogressbar=optiondict["showprogressbar"],
+        chunksize=optiondict["mp_chunksize"],
+        despeckle_thresh=optiondict["despeckle_thresh"],
+        initiallags=initlags,
+        rt_floatset=rt_floatset,
+        rt_floattype=rt_floattype,
+    )
+    enablemkl(optiondict["mklthreads"], debug=threaddebug)
+
+    TimingLGR.info(
+        f"Time lag estimation end, pass {thepass}",
+        {
+            "message2": voxelsprocessed_fc,
+            "message3": "voxels",
+        },
+    )
+
+    # Step 2b - Correlation time despeckle
+    if optiondict["despeckle_passes"] > 0:
+        LGR.info(f"\n\n{similaritytype} despeckling pass {thepass}")
+        LGR.info(f"\tUsing despeckle_thresh = {optiondict['despeckle_thresh']:.3f}")
+        TimingLGR.info(f"{similaritytype} despeckle start, pass {thepass}")
+
+        # find lags that are very different from their neighbors, and refit starting at the median lag for the point
+        voxelsprocessed_fc_ds = 0
+        despecklingdone = False
+        lastnumdespeckled = 1000000
+        for despecklepass in range(optiondict["despeckle_passes"]):
+            LGR.info(f"\n\n{similaritytype} despeckling subpass {despecklepass + 1}")
+            outmaparray *= 0.0
+            outmaparray[validvoxels] = eval("lagtimes")[:]
+
+            # find voxels to despeckle
+            medianlags = ndimage.median_filter(outmaparray.reshape(nativespaceshape), 3).reshape(
+                numspatiallocs
+            )
+            # voxels that we're happy with have initlags set to -1000000.0
+            initlags = np.where(
+                np.abs(outmaparray - medianlags) > optiondict["despeckle_thresh"],
+                medianlags,
+                -1000000.0,
+            )[validvoxels]
+
+            if len(initlags) > 0:
+                numdespeckled = len(np.where(initlags != -1000000.0)[0])
+                if lastnumdespeckled > numdespeckled > 0:
+                    lastnumdespeckled = numdespeckled
+                    disablemkl(optiondict["nprocs_fitcorr"], debug=threaddebug)
+                    voxelsprocessed_thispass = tide_simfuncfit.fitcorr(
+                        trimmedcorrscale,
+                        theFitter,
+                        corrout,
+                        fitmask,
+                        failreason,
+                        lagtimes,
+                        lagstrengths,
+                        lagsigma,
+                        gaussout,
+                        windowout,
+                        R2,
+                        despeckling=True,
+                        peakdict=thepeakdict,
+                        nprocs=optiondict["nprocs_fitcorr"],
+                        alwaysmultiproc=optiondict["alwaysmultiproc"],
+                        fixdelay=optiondict["fixdelay"],
+                        initialdelayvalue=theinitialdelay,
+                        showprogressbar=optiondict["showprogressbar"],
+                        chunksize=optiondict["mp_chunksize"],
+                        despeckle_thresh=optiondict["despeckle_thresh"],
+                        initiallags=initlags,
+                        rt_floatset=rt_floatset,
+                        rt_floattype=rt_floattype,
+                    )
+                    enablemkl(optiondict["mklthreads"], debug=threaddebug)
+
+                    voxelsprocessed_fc_ds += voxelsprocessed_thispass
+                    optiondict[
+                        "despecklemasksize_pass" + str(thepass) + "_d" + str(despecklepass + 1)
+                    ] = voxelsprocessed_thispass
+                    optiondict[
+                        "despecklemaskpct_pass" + str(thepass) + "_d" + str(despecklepass + 1)
+                    ] = (100.0 * voxelsprocessed_thispass / optiondict["corrmasksize"])
+                else:
+                    despecklingdone = True
+            else:
+                despecklingdone = True
+            if despecklingdone:
+                LGR.info("Nothing left to do! Terminating despeckling")
+                break
+
+        internaldespeckleincludemask = np.where(
+            np.abs(outmaparray - medianlags) > optiondict["despeckle_thresh"],
+            medianlags,
+            0.0,
+        )
+        if optiondict["savedespecklemasks"] and (optiondict["despeckle_passes"] > 0):
+            despecklesavemask = np.where(internaldespeckleincludemask[validvoxels] == 0.0, 0, 1)
+            if thepass == optiondict["passes"]:
+                if not optiondict["textio"]:
+                    if fileiscifti:
+                        timeindex = theheader["dim"][0] - 1
+                        spaceindex = theheader["dim"][0]
+                        theheader["dim"][timeindex] = 1
+                        theheader["dim"][spaceindex] = numspatiallocs
+                    else:
+                        theheader["dim"][0] = 3
+                        theheader["dim"][4] = 1
+                        theheader["pixdim"][4] = 1.0
+                masklist = [
+                    (
+                        despecklesavemask,
+                        "despeckle",
+                        "mask",
+                        None,
+                        "Voxels that underwent despeckling in the final pass",
+                    )
+                ]
+                tide_io.savemaplist(
+                    outputname,
+                    masklist,
+                    validvoxels,
+                    nativespaceshape,
+                    theheader,
+                    bidsbasedict,
+                    textio=optiondict["textio"],
+                    fileiscifti=fileiscifti,
+                    rt_floattype=rt_floattype,
+                    cifti_hdr=cifti_hdr,
+                )
+        LGR.info(
+            f"\n\n{voxelsprocessed_fc_ds} voxels despeckled in "
+            f"{optiondict['despeckle_passes']} passes"
+        )
+        TimingLGR.info(
+            f"{similaritytype} despeckle end, pass {thepass}",
+            {
+                "message2": voxelsprocessed_fc_ds,
+                "message3": "voxels",
+            },
+        )
+
+    # Step 2c - patch shifting
+    if optiondict["patchshift"]:
+        outmaparray *= 0.0
+        outmaparray[validvoxels] = eval("lagtimes")[:]
+        # new method
+        masklist = [
+            (
+                outmaparray[validvoxels],
+                f"lagtimes_prepatch_pass{thepass}",
+                "map",
+                None,
+                f"Input lagtimes map prior to patch map generation pass {thepass}",
+            ),
+        ]
+        tide_io.savemaplist(
+            outputname,
+            masklist,
+            validvoxels,
+            nativespaceshape,
+            theheader,
+            bidsbasedict,
+            textio=optiondict["textio"],
+            fileiscifti=fileiscifti,
+            rt_floattype=rt_floattype,
+            cifti_hdr=cifti_hdr,
+        )
+
+        # create list of anomalous 3D regions that don't match surroundings
+        if nim_affine is not None:
+            # make an atlas of anomalous patches - each patch shares the same integer value
+            step1 = tide_patch.calc_DoG(
+                outmaparray.reshape(nativespaceshape).copy(),
+                nim_affine,
+                thesizes,
+                fwhm=optiondict["patchfwhm"],
+                ratioopt=False,
+                debug=True,
+            )
+            masklist = [
+                (
+                    step1.reshape(internalspaceshape)[validvoxels],
+                    f"DoG_pass{thepass}",
+                    "map",
+                    None,
+                    f"DoG map for pass {thepass}",
+                ),
+            ]
+            tide_io.savemaplist(
+                outputname,
+                masklist,
+                validvoxels,
+                nativespaceshape,
+                theheader,
+                bidsbasedict,
+                textio=optiondict["textio"],
+                fileiscifti=fileiscifti,
+                rt_floattype=rt_floattype,
+                cifti_hdr=cifti_hdr,
+            )
+            step2 = tide_patch.invertedflood3D(
+                step1,
+                1,
+            )
+            masklist = [
+                (
+                    step2.reshape(internalspaceshape)[validvoxels],
+                    f"invertflood_pass{thepass}",
+                    "map",
+                    None,
+                    f"Inverted flood map for pass {thepass}",
+                ),
+            ]
+            tide_io.savemaplist(
+                outputname,
+                masklist,
+                validvoxels,
+                nativespaceshape,
+                theheader,
+                bidsbasedict,
+                textio=optiondict["textio"],
+                fileiscifti=fileiscifti,
+                rt_floattype=rt_floattype,
+                cifti_hdr=cifti_hdr,
+            )
+
+            patchmap = tide_patch.separateclusters(
+                step2,
+                sizethresh=optiondict["patchminsize"],
+                debug=True,
+            )
+            # patchmap = tide_patch.getclusters(
+            #   outmaparray.reshape(nativespaceshape),
+            #    nim_affine,
+            #    thesizes,
+            #    fwhm=optiondict["patchfwhm"],
+            #    ratioopt=True,
+            #    sizethresh=optiondict["patchminsize"],
+            #    debug=True,
+            # )
+            masklist = [
+                (
+                    patchmap[validvoxels],
+                    f"patch_pass{thepass}",
+                    "map",
+                    None,
+                    f"Patch map for despeckling pass {thepass}",
+                ),
+            ]
+            tide_io.savemaplist(
+                outputname,
+                masklist,
+                validvoxels,
+                nativespaceshape,
+                theheader,
+                bidsbasedict,
+                textio=optiondict["textio"],
+                fileiscifti=fileiscifti,
+                rt_floattype=rt_floattype,
+                cifti_hdr=cifti_hdr,
+            )
+
+        # now shift the patches to align with the majority of the image
+        tide_patch.interppatch(lagtimes, patchmap[validvoxels])

rapidtide/workflows/delayvar.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   Copyright 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.

rapidtide/workflows/diffrois.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/endtidalproc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/fdica.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/filtnifti.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/filttc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/fixtr.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.

rapidtide/workflows/gmscalc.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2016-2024 Blaise Frederick
+#   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.