rapidtide 2.9.6__py3-none-any.whl → 3.1.3__py3-none-any.whl

rapidtide/scripts/{spatialmi → spatialmi.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.spatialmi as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.spatialmi)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{spectrogram → spectrogram.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.spectrogram as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.spectrogram)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/stupidramtricks.py

@@ -0,0 +1,238 @@
+#!/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 os
+
+import numpy as np
+
+import rapidtide.multiproc as tide_multiproc
+import rapidtide.refinedelay as tide_refinedelay
+import rapidtide.util as tide_util
+import rapidtide.workflows.parser_funcs as pf
+
+
+def _get_parser():
+    """
+    Argument parser for stupidramtricks
+    """
+    parser = argparse.ArgumentParser(
+        prog="stupidramtricks",
+        description="Make shared memory blocks, do something with them.",
+        allow_abbrev=False,
+    )
+
+    # Required arguments
+    parser.add_argument(
+        "--numvoxels",
+        dest="numvoxels",
+        action="store",
+        type=int,
+        metavar="NUMVOXELS",
+        help=("Set blocks to have NUMVOXELS voxels."),
+        default=230000,
+    )
+    # Required arguments
+    parser.add_argument(
+        "--numtimepoints",
+        dest="numtimepoints",
+        action="store",
+        type=int,
+        metavar="NUMPOINTS",
+        help=("Set blocks to have NUMPOINTS timespoints."),
+        default=500,
+    )
+
+    parser.add_argument(
+        "--nprocs",
+        dest="nprocs",
+        action="store",
+        type=int,
+        metavar="NPROCS",
+        help=(
+            "Use NPROCS worker processes for multiprocessing. "
+            "Setting NPROCS to less than 1 sets the number of "
+            "worker processes to n_cpus."
+        ),
+        default=1,
+    )
+    parser.add_argument(
+        "--usesharedmem",
+        dest="usesharedmem",
+        action="store_true",
+        help=("Use shared memory"),
+        default=False,
+    )
+    parser.add_argument(
+        "--debug",
+        dest="debug",
+        action="store_true",
+        help=("Print debug messages"),
+        default=False,
+    )
+
+    return parser
+
+
+def stupidramtricks(args):
+    # get the pid of the parent process
+    args.pid = os.getpid()
+
+    args.internalprecision = "single"
+    args.outputprecision = "double"
+
+    print("Start")
+
+    if args.nprocs < 1:
+        args.nprocs = tide_multiproc.maxcpus()
+
+    if args.internalprecision == "double":
+        rt_floattype = np.float64
+    else:
+        rt_floattype = np.float32
+
+    # set the output precision
+    if args.outputprecision == "double":
+        rt_outfloattype = np.float64
+    else:
+        rt_outfloattype = np.float32
+
+    # select the voxels in the mask
+    print("setting sizes")
+    numvalidspatiallocs = args.numvoxels
+    if args.debug:
+        print(f"{numvalidspatiallocs=}")
+    internalvalidspaceshape = numvalidspatiallocs
+    derivaxissize = 2
+    internalvalidspaceshapederivs = (
+        internalvalidspaceshape,
+        derivaxissize,
+    )
+    internalvalidfmrishape = (numvalidspatiallocs, args.numtimepoints)
+    if args.debug:
+        print(f"validvoxels shape = {numvalidspatiallocs}")
+        print(f"internalvalidfmrishape shape = {internalvalidfmrishape}")
+
+    fmridata = np.zeros(internalvalidfmrishape, dtype=rt_outfloattype)
+
+    if args.usesharedmem:
+        if args.debug:
+            print("allocating shared memory")
+        # first move fmridata into shared memory
+        fmridata, fmridata_shm = tide_util.numpy2shared(
+            fmridata, rt_floattype, name=f"fmridata_{args.pid}"
+        )
+        sLFOfitmean, sLFOfitmean_shm = tide_util.allocshared(
+            internalvalidspaceshape, rt_outfloattype
+        )
+        rvalue, rvalue_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloattype)
+        r2value, r2value_shm = tide_util.allocshared(internalvalidspaceshape, rt_outfloattype)
+        fitNorm, fitNorm_shm = tide_util.allocshared(
+            internalvalidspaceshapederivs, rt_outfloattype
+        )
+        fitcoeff, fitcoeff_shm = tide_util.allocshared(
+            internalvalidspaceshapederivs, rt_outfloattype
+        )
+        movingsignal, movingsignal_shm = tide_util.allocshared(
+            internalvalidfmrishape, rt_outfloattype
+        )
+        lagtc, lagtc_shm = tide_util.allocshared(internalvalidfmrishape, rt_floattype)
+        filtereddata, filtereddata_shm = tide_util.allocshared(
+            internalvalidfmrishape, rt_outfloattype
+        )
+
+        location = "in shared memory"
+    else:
+        if args.debug:
+            print("allocating memory")
+        sLFOfitmean = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
+        rvalue = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
+        r2value = np.zeros(internalvalidspaceshape, dtype=rt_outfloattype)
+        fitNorm = np.zeros(internalvalidspaceshapederivs, dtype=rt_outfloattype)
+        fitcoeff = np.zeros(internalvalidspaceshapederivs, dtype=rt_outfloattype)
+        movingsignal = np.zeros(internalvalidfmrishape, dtype=rt_outfloattype)
+        lagtc = np.zeros(internalvalidfmrishape, dtype=rt_floattype)
+        filtereddata = np.zeros(internalvalidfmrishape, dtype=rt_outfloattype)
+        location = "locally"
+
+    totalbytes = (
+        fmridata.nbytes
+        + sLFOfitmean.nbytes
+        + rvalue.nbytes
+        + r2value.nbytes
+        + fitNorm.nbytes
+        + fitcoeff.nbytes
+        + movingsignal.nbytes
+        + lagtc.nbytes
+        + filtereddata.nbytes
+    )
+
+    thesize, theunit = tide_util.format_bytes(totalbytes)
+    print(f"allocated {thesize:.3f} {theunit} {location}")
+
+    """regressderivratios, regressrvalues = tide_refinedelay.getderivratios(
+        fmri_data_valid,
+        validvoxels,
+        initial_fmri_x,
+        lagtimes_valid,
+        corrmask_valid,
+        genlagtc,
+        mode,
+        outputname,
+        oversamptr,
+        sLFOfitmean,
+        rvalue,
+        r2value,
+        fitNorm[:, :2],
+        fitcoeff[:, :2],
+        movingsignal,
+        lagtc,
+        filtereddata,
+        LGR,
+        TimingLGR,
+        therunoptions,
+        debug=args.debug,
+    )"""
+
+    # clean up shared memory
+    if args.usesharedmem:
+        tide_util.cleanup_shm(fmridata_shm)
+        tide_util.cleanup_shm(sLFOfitmean_shm)
+        tide_util.cleanup_shm(rvalue_shm)
+        tide_util.cleanup_shm(r2value_shm)
+        tide_util.cleanup_shm(fitNorm_shm)
+        tide_util.cleanup_shm(fitcoeff_shm)
+        tide_util.cleanup_shm(movingsignal_shm)
+        tide_util.cleanup_shm(lagtc_shm)
+        tide_util.cleanup_shm(filtereddata_shm)
+
+
+def process_args(inputargs=None):
+    """
+    Compile arguments for stupidramtrics workflow.
+    """
+    args, argstowrite = pf.setargs(_get_parser, inputargs=inputargs)
+    return args
+
+
+def entrypoint():
+    pf.generic_init(_get_parser, stupidramtricks)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{synthASL → synthASL.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.synthASL as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.synthASL)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{tcfrom2col → tcfrom2col.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.tcfrom2col as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.tcfrom2col)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{tcfrom3col → tcfrom3col.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.tcfrom3col as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.tcfrom3col)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{temporaldecomp → temporaldecomp.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.niftidecomp as theworkflow
 import rapidtide.workflows.parser_funcs as pf
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser_temporal, theworkflow.main_temporal)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{testhrv → testhrv.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/scripts/{threeD → threeD.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.
@@ -231,6 +231,11 @@ def on_key_press(event):
 # def on_draw(ev):
 # canvas.update()
 
-if __name__ == "__main__":
+
+def entrypoint():
     print(__doc__)
     app.run()
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{tidepool → tidepool.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.tidepool as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.tidepool)
+
+
+if __name__ == "__main__":
+    entrypoint()

rapidtide/scripts/{variabilityizer → variabilityizer.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.
@@ -19,5 +19,10 @@
 import rapidtide.workflows.parser_funcs as pf
 import rapidtide.workflows.variabilityizer as theworkflow
 
-if __name__ == "__main__":
+
+def entrypoint():
     pf.generic_init(theworkflow._get_parser, theworkflow.variabilityizer)
+
+
+if __name__ == "__main__":
+    entrypoint()