rapidtide 3.0a14__py3-none-any.whl → 3.0.1__py3-none-any.whl

rapidtide/tests/test_fullrunrapidtide_v6.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/tests/test_io.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/tests/test_linfitfiltpass.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/tests/test_mi.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/tests/test_miscmath.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/tests/test_motionregress.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/tests/test_nullcorr.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/tests/test_padvec.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/tests/test_phaseanalysis.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2018-2024 Blaise Frederick
+#   Copyright 2018-2025 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/tests/test_rapidtideparser.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/tests/test_refinedelay.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.
@@ -151,7 +151,6 @@ def eval_refinedelay(
         "mp_chunksize": 1000,
         "showprogressbar": False,
         "alwaysmultiproc": False,
-        "memprofile": False,
         "focaldebug": debug,
         "fmrifreq": Fs,
         "textio": False,

rapidtide/tests/test_runmisc.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/tests/test_sharedmem.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/tests/test_simulate.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 # -*- coding: utf-8 -*-
 #
-#   Copyright 2017-2024 Blaise Frederick
+#   Copyright 2017-2025 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/tests/test_stcorrelate.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/tests/test_timeshift.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/tests/test_valtoindex.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/tests/test_zRapidtideDataset.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/tests/utils.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/transformerdlfilter.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.
@@ -16,9 +16,7 @@
 #   limitations under the License.
 #
 #
-"""This module contains all an alternate filter routine
-
-"""
+"""This module contains all an alternate filter routine"""
 import tensorflow as tf
 from tensorflow.keras.layers import (
     Dense,

rapidtide/util.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.
@@ -35,6 +35,13 @@ import pandas as pd
 import rapidtide._version as tide_versioneer
 import rapidtide.io as tide_io
 
+try:
+    import mkl
+
+    mklexists = True
+except ImportError:
+    mklexists = False
+
 LGR = logging.getLogger(__name__)
 TimingLGR = logging.getLogger("TIMING")
 MemoryLGR = logging.getLogger("MEMORY")
@@ -46,13 +53,6 @@ MAXLINES = 10000000
 donotbeaggressive = True
 
 # ----------------------------------------- Conditional imports ---------------------------------------
-try:
-    from memory_profiler import profile
-
-    memprofilerexists = True
-except ImportError:
-    memprofilerexists = False
-
 try:
     from numba import jit
 except ImportError:
@@ -69,12 +69,6 @@ else:
 
 
 def checkimports(optiondict):
-    if memprofilerexists:
-        print("memprofiler exists")
-    else:
-        print("memprofiler does not exist")
-    optiondict["memprofilerexists"] = memprofilerexists
-
     if pyfftwpresent:
         print("pfftw exists")
     else:
@@ -119,6 +113,21 @@ def disablenumba():
     donotusenumba = True
 
 
+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)
+
+
 # --------------------------- Utility functions -------------------------------------------------
 def findavailablemem():
     if os.path.isfile("/sys/fs/cgroup/memory/memory.limit_in_bytes"):
@@ -292,6 +301,20 @@ def isexecutable(command):
         )
 
 
+def makeadir(pathname):
+    try:
+        os.makedirs(pathname)
+    except OSError:
+        if os.path.exists(pathname):
+            # We are nearly safe
+            return True
+        else:
+            # There was an error on creation, so make sure we know about it
+            print("ERROR: ", pathname, " does not exist, and could not create it")
+            return False
+    return True
+
+
 def findreferencedir():
     # Get the list of directories
     site_packages_dirs = site.getsitepackages()

rapidtide/voxelData.py

@@ -0,0 +1,278 @@
+#!/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 numpy as np
+from tf_keras.src.layers.preprocessing.benchmarks.index_lookup_forward_benchmark import (
+    get_vocab,
+)
+from tqdm import tqdm
+
+import rapidtide.filter as tide_filt
+import rapidtide.io as tide_io
+
+
+class VoxelData:
+    nim = None
+    nim_data = None
+    nim_hdr = None
+    nim_affine = None
+    theshape = None
+    xsize = None
+    ysize = None
+    numslices = None
+    timepoints = None
+    xdim = None
+    ydim = None
+    slicethickness = None
+    timestep = None
+    thesizes = None
+    thedims = None
+    numspatiallocs = None
+    nativespaceshape = None
+    validvoxels = None
+    cifti_hdr = None
+    filetype = None
+    resident = False
+
+    def __init__(
+        self,
+        filename,
+        timestep=0.0,
+        validstart=None,
+        validend=None,
+    ):
+
+        self.filename = filename
+        self.readdata(timestep, validstart, validend)
+
+    def readdata(self, timestep, validstart, validend):
+        self.load()
+
+        if tide_io.checkiftext(self.filename):
+            self.filetype = "text"
+            self.nim_hdr = None
+            self.nim_affine = None
+            self.theshape = np.shape(self.nim_data)
+            self.xsize = self.theshape[0]
+            self.ysize = 1
+            self.numslices = 1
+            self.timepoints = self.theshape[1]
+            self.thesizes = [0, int(self.xsize), 1, 1, int(self.timepoints)]
+            self.toffset = 0.0
+            self.numspatiallocs = int(self.xsize)
+            self.nativespaceshape = self.xsize
+            self.cifti_hdr = None
+        else:
+            if tide_io.checkifcifti(self.filename):
+                self.filetype = "cifti"
+                self.nim_affine = None
+                self.timepoints = self.nim_data.shape[1]
+                self.numspatiallocs = self.nim_data.shape[0]
+                self.nativespaceshape = (1, 1, 1, 1, self.numspatiallocs)
+            else:
+                self.filetype = "nifti"
+                self.nim_affine = self.nim.affine
+                self.xsize, self.ysize, self.numslices, self.timepoints = tide_io.parseniftidims(
+                    self.thedims
+                )
+                self.numspatiallocs = int(self.xsize) * int(self.ysize) * int(self.numslices)
+                self.cifti_hdr = None
+                self.nativespaceshape = (self.xsize, self.ysize, self.numslices)
+            self.xdim, self.ydim, self.slicethickness, dummy = tide_io.parseniftisizes(
+                self.thesizes
+            )
+
+        # correct some fields if necessary
+        if self.filetype == "cifti":
+            self.timestep = 0.72  # this is wrong and is a hack until I can parse CIFTI XML
+            self.toffset = 0.0
+        else:
+            if self.filetype == "text":
+                if timestep <= 0.0:
+                    raise ValueError(
+                        "for text file data input, you must use the -t option to set the timestep"
+                    )
+            else:
+                if self.nim_hdr.get_xyzt_units()[1] == "msec":
+                    self.timestep = self.thesizes[4] / 1000.0
+                    self.toffset = self.nim_hdr["toffset"] / 1000.0
+                else:
+                    self.timestep = self.thesizes[4]
+                    self.toffset = self.nim_hdr["toffset"]
+        if timestep > 0.0:
+            self.timestep = timestep
+
+        self.setvalidtimes(validstart, validend)
+        self.resident = True
+
+    def getsizes(self):
+        return self.xdim, self.ydim, self.slicethickness, self.timestep
+
+    def getdims(self):
+        return self.xsize, self.ysize, self.numslices, self.timepoints
+
+    def unload(self):
+        del self.nim_data
+        del self.nim
+        self.resident = False
+
+    def load(self):
+        if self.filetype is not None:
+            print("reloading non-resident data")
+        else:
+            print(f"loading data from {self.filename}")
+        if tide_io.checkiftext(self.filename):
+            self.nim_data = tide_io.readvecs(self.filename)
+            self.nim = None
+        else:
+            if tide_io.checkifcifti(self.filename):
+                self.filetype = "cifti"
+                (
+                    dummy,
+                    self.cifti_hdr,
+                    self.nim_data,
+                    self.nim_hdr,
+                    self.thedims,
+                    self.thesizes,
+                    dummy,
+                ) = tide_io.readfromcifti(self.filename)
+                self.nim = None
+            else:
+                self.nim, self.nim_data, self.nim_hdr, self.thedims, self.thesizes = (
+                    tide_io.readfromnifti(self.filename)
+                )
+        self.resident = True
+
+    def setvalidtimes(self, validstart, validend):
+        if validstart is None:
+            self.validstart = 0
+        else:
+            self.validstart = validstart
+        if validend is None:
+            self.validend = self.timepoints - 1
+        else:
+            self.validend = validend
+
+    def setvalidvoxels(self, validvoxels):
+        self.validvoxels = validvoxels
+        self.numvalidspatiallocs = np.shape(self.validvoxels)[0]
+
+    def native(self):
+        if not self.resident:
+            self.load()
+        return self.nim_data
+
+    def nativetrimmed(self):
+        if not self.resident:
+            self.load()
+        if self.filetype == "nifti":
+            return self.nim_data[:, :, :, self.validstart : self.validend + 1]
+        else:
+            return self.nim_data[:, self.validstart: self.validend + 1]
+
+    def voxelbytime(self):
+        return self.nativetrimmed().reshape(self.numspatiallocs, -1)
+
+    def getvalidvoxels(self):
+        if self.validvoxels is None:
+            return self.voxelbytime()
+        else:
+            return self.voxelbytime()[self.validvoxels, :]
+
+    def smooth(
+        self,
+        gausssigma,
+        brainmask=None,
+        graymask=None,
+        whitemask=None,
+        premask=False,
+        premasktissueonly=False,
+        showprogressbar=False,
+    ):
+        # do spatial filtering if requested
+        if self.filetype == "cifti" or self.filetype == "text":
+            gausssigma = 0.0
+        if gausssigma < 0.0:
+            # set gausssigma automatically
+            gausssigma = np.mean([self.xdim, self.ydim, self.slicethickness]) / 2.0
+        if gausssigma > 0.0:
+            # premask data if requested
+            if premask:
+                if premasktissueonly:
+                    if (graymask is not None) and (whitemask is not None):
+                        multmask = graymask + whitemask
+                    else:
+                        raise ValueError(
+                            "ERROR: graymask and whitemask must be defined to use premasktissueonly - exiting"
+                        )
+                else:
+                    if brainmask is not None:
+                        multmask = brainmask
+                    else:
+                        raise ValueError(
+                            "ERROR: brainmask must be defined to use premask - exiting"
+                        )
+                print(f"premasking timepoints {self.validstart} to {self.validend}")
+                for i in tqdm(
+                    range(self.validstart, self.validend + 1),
+                    desc="Timepoint",
+                    unit="timepoints",
+                    disable=(not showprogressbar),
+                ):
+                    self.nim_data[:, :, :, i] *= multmask
+
+            # now apply the filter
+            print(
+                f"applying gaussian spatial filter to timepoints {self.validstart} "
+                f"to {self.validend} with sigma={gausssigma}"
+            )
+            sourcedata = self.native()
+            for i in tqdm(
+                range(self.validstart, self.validend + 1),
+                desc="Timepoint",
+                unit="timepoints",
+                disable=(not showprogressbar),
+            ):
+                self.nim_data[:, :, :, i] = tide_filt.ssmooth(
+                    self.xdim,
+                    self.ydim,
+                    self.slicethickness,
+                    gausssigma,
+                    sourcedata[:, :, :, i],
+                )
+        return gausssigma
+
+    def summarize(self):
+        print("Voxel data summary:")
+        print(f"\t{self.nim=}")
+        print(f"\t{self.nim_data.shape=}")
+        print(f"\t{self.nim_hdr=}")
+        print(f"\t{self.nim_affine=}")
+        print(f"\t{self.theshape=}")
+        print(f"\t{self.xsize=}")
+        print(f"\t{self.ysize=}")
+        print(f"\t{self.numslices=}")
+        print(f"\t{self.timepoints=}")
+        print(f"\t{self.timestep=}")
+        print(f"\t{self.thesizes=}")
+        print(f"\t{self.thedims=}")
+        print(f"\t{self.numspatiallocs=}")
+        print(f"\t{self.nativespaceshape=}")
+        print(f"\t{self.cifti_hdr=}")
+        print(f"\t{self.filetype=}")
+        print(f"\t{self.resident=}")

rapidtide/wiener.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/wiener2.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/adjustoffset.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/aligntcs.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.