rapidtide 3.1__py3-none-any.whl → 3.1.1__py3-none-any.whl

rapidtide/workflows/refineRegressor.py

@@ -87,8 +87,7 @@ class RegressorRefiner:
         prewhitenregressor: bool = False,
         prewhitenlags: int = 10,
         debug: bool = False,
-        rt_floattype: str = "float64",
-        rt_floatset: Any = np.float64,
+        rt_floattype: np.dtype = np.float64,
     ) -> None:
         """
         Initialize the object with configuration parameters for fMRI data processing.
@@ -188,10 +187,8 @@ class RegressorRefiner:
             Number of lags for pre-whitening (default is 10).
         debug : bool, optional
             Enable debug mode (default is False).
-        rt_floattype : str, optional
-            Real-time floating-point data type (default is "float64").
-        rt_floatset : Any, optional
-            Real-time float type setting (default is np.float64).
+        rt_floattype : np.dtype, optional
+            Rapidtide floating-point data type (default is np.float64).
 
         Returns
         -------
@@ -252,8 +249,7 @@ class RegressorRefiner:
         ...     prewhitenregressor=True,
         ...     prewhitenlags=5,
         ...     debug=False,
-        ...     rt_floattype="float32",
-        ...     rt_floatset=np.float32,
+        ...     rt_floattype=np.float32,
         ... )
         """
         self.internalvalidfmrishape = internalvalidfmrishape
@@ -300,7 +296,6 @@ class RegressorRefiner:
         self.prewhitenlags = prewhitenlags
         self.debug = debug
         self.rt_floattype = rt_floattype
-        self.rt_floatset = rt_floatset
 
         self.setmasks(includemask, excludemask)
         self.totalrefinementbytes = self._allocatemem(pid)
@@ -638,7 +633,6 @@ class RegressorRefiner:
             showprogressbar=self.showprogressbar,
             chunksize=self.chunksize,
             padtrs=self.padtrs,
-            rt_floatset=self.rt_floatset,
             rt_floattype=self.rt_floattype,
         )
         return voxelsprocessed_rra
@@ -781,7 +775,6 @@ class RegressorRefiner:
             windowfunc=self.windowfunc,
             cleanrefined=self.cleanrefined,
             bipolar=self.bipolar,
-            rt_floatset=self.rt_floatset,
             rt_floattype=self.rt_floattype,
         )
         outputdict = {}
@@ -976,8 +969,7 @@ def refineRegressor(
     outputname: Any,
     nativefmrishape: Any,
     bidsbasedict: Any,
-    rt_floatset: Any = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
     debug: bool = False,
 ) -> None:
     """
@@ -1042,10 +1034,8 @@ def refineRegressor(
         Shape of the native fMRI data.
     bidsbasedict : dict
         Dictionary for BIDS metadata.
-    rt_floatset : numpy.dtype, optional
+    rt_floattype : numpy.dtype, optional
         Data type for floating-point operations, default is np.float64.
-    rt_floattype : str, optional
-        String representation of floating-point data type, default is "float64".
     debug : bool, optional
         Enable debug mode, default is False.
 

rapidtide/workflows/regressfrommaps.py

@@ -57,6 +57,7 @@ def regressfrommaps(
     alwaysmultiproc: bool = False,
     saveEVsandquit: bool = False,
     coefficientsonly: bool = False,
+    timemask: Optional[NDArray] = None,
     debug: bool = False,
 ) -> None:
     """
@@ -127,6 +128,8 @@ def regressfrommaps(
         Save EVs and quit early (default is False).
     coefficientsonly : bool, optional
         Return only coefficients (default is False).
+    timemask : NDArray, optional
+       Mask of timepoints to include in regression filtering.
     debug : bool, optional
         Enable debug output (default is False).
 
@@ -189,8 +192,7 @@ def regressfrommaps(
         print(f"\t{outputname=}")
         print(f"\t{oversamptr=}")
         print(f"\t{regressfiltthreshval=}")
-    rt_floatset = np.float64
-    rt_floattype = "float64"
+    rt_floattype = np.float64
     numvalidspatiallocs = np.shape(validvoxels)[0]
 
     # generate the voxel specific regressors
@@ -210,10 +212,12 @@ def regressfrommaps(
         alwaysmultiproc=alwaysmultiproc,
         showprogressbar=showprogressbar,
         chunksize=chunksize,
-        rt_floatset=rt_floatset,
         rt_floattype=rt_floattype,
         debug=debug,
     )
+    if timemask is not None:
+        lagtc = lagtc * timemask[None, :]
+
     if debug:
         print(f"\t{lagtimes.shape=}")
         threshmask = np.where(fitmask > 0, 1, 0)
@@ -234,7 +238,7 @@ def regressfrommaps(
         if debug:
             print(f"adding derivatives up to order {regressderivs} prior to regression")
         regressorset = tide_linfitfiltpass.makevoxelspecificderivs(lagtc, regressderivs)
-        baseev = rt_floatset(genlagtc.yfromx(initial_fmri_x))
+        baseev = (genlagtc.yfromx(initial_fmri_x)).astype(rt_floattype)
         evset = tide_linfitfiltpass.makevoxelspecificderivs(
             baseev.reshape((1, -1)), regressderivs
         ).reshape((-1, 2))
@@ -242,7 +246,7 @@ def regressfrommaps(
         if debug:
             print(f"using raw lagged regressors for regression")
         regressorset = lagtc
-        evset = rt_floatset(genlagtc.yfromx(initial_fmri_x))
+        evset = (genlagtc.yfromx(initial_fmri_x)).astype(rt_floattype)
     if debug:
         print(f"{regressorset.shape=}")
 
@@ -273,7 +277,6 @@ def regressfrommaps(
         showprogressbar=showprogressbar,
         verbose=(LGR is not None),
         chunksize=chunksize,
-        rt_floatset=rt_floatset,
         rt_floattype=rt_floattype,
         debug=debug,
     )

rapidtide/workflows/retrolagtcs.py

@@ -215,10 +215,8 @@ def retrolagtcs(args: Any) -> None:
     ... )
     >>> retrolagtcs(args)
     """
-    rt_floatset = np.float64
-    rt_floattype = "float64"
-    rt_outfloatset = np.float64
-    rt_outfloattype = "float64"
+    rt_floattype = np.float64
+    rt_outfloattype = np.float64
 
     # get the pid of the parent process
     args.pid = os.getpid()
@@ -318,13 +316,13 @@ def retrolagtcs(args: Any) -> None:
         if args.debug:
             print("allocating memory")
     fitNorm, fitNorm_shm = tide_util.allocarray(
-        internalvalidspaceshapederivs, rt_outfloatset, shared=usesharedmem
+        internalvalidspaceshapederivs, rt_outfloattype, shared=usesharedmem
     )
     fitcoeff, fitcoeff_shm = tide_util.allocarray(
-        internalvalidspaceshapederivs, rt_outfloatset, shared=usesharedmem
+        internalvalidspaceshapederivs, rt_outfloattype, shared=usesharedmem
     )
     lagtc, lagtc_shm = tide_util.allocarray(
-        internalvalidfmrishape, rt_floatset, shared=usesharedmem
+        internalvalidfmrishape, rt_floattype, shared=usesharedmem
     )
 
     outputpath = os.path.dirname(args.outputroot)

rapidtide/workflows/retroregress.py

@@ -414,7 +414,7 @@ def retroregress(args: Any) -> None:
     # save the raw and formatted command lines
     argstowrite = sys.argv
     thecommandline = " ".join(sys.argv[1:])
-    tide_io.writevec([thecommandline], f"{outputname}_retrocommandline.txt")
+    tide_io.writevec(np.asarray([thecommandline]), f"{outputname}_retrocommandline.txt")
     formattedcommandline = []
     for thetoken in argstowrite[0:3]:
         formattedcommandline.append(thetoken)
@@ -433,7 +433,9 @@ def retroregress(args: Any) -> None:
         else:
             suffix = ""
         formattedcommandline[i] = prefix + formattedcommandline[i] + suffix
-    tide_io.writevec(formattedcommandline, f"{outputname}_retroformattedcommandline.txt")
+    tide_io.writevec(
+        np.asarray(formattedcommandline), f"{outputname}_retroformattedcommandline.txt"
+    )
 
     if args.nprocs < 1:
         args.nprocs = tide_multiproc.maxcpus()
@@ -469,19 +471,15 @@ def retroregress(args: Any) -> None:
         sys.exit()
 
     if therunoptions["internalprecision"] == "double":
-        rt_floattype = "float64"
-        rt_floatset = np.float64
+        rt_floattype = np.float64
     else:
-        rt_floattype = "float32"
-        rt_floatset = np.float32
+        rt_floattype = np.float32
 
     # set the output precision
     if therunoptions["outputprecision"] == "double":
-        rt_outfloattype = "float64"
-        rt_outfloatset = np.float64
+        rt_outfloattype = np.float64
     else:
-        rt_outfloattype = "float32"
-        rt_outfloatset = np.float32
+        rt_outfloattype = np.float32
     therunoptions["saveminimumsLFOfiltfiles"] = args.saveminimumsLFOfiltfiles
 
     # read the fmri input files
@@ -773,7 +771,6 @@ def retroregress(args: Any) -> None:
                 maxdelay=args.maxdelay,
                 numpoints=args.numpoints,
                 histlen=therunoptions["histlen"],
-                rt_floatset=rt_floatset,
                 rt_floattype=rt_floattype,
                 debug=args.debug,
             )
@@ -1058,13 +1055,10 @@ def retroregress(args: Any) -> None:
                 (initialvariance, "lfofilterInbandVarianceBefore", "map", None),
                 (finalvariance, "lfofilterInbandVarianceAfter", "map", None),
                 (varchange, "CVRVariance", "map", None),
+                (rvalue, "CVRR", "map", None),
+                (r2value, "CVRR2", "map", None),
+                (fitcoeff[:, 0], "CVR", "map", "percent"),
             ]
-            if args.savenormalsLFOfiltfiles:
-                maplist += [
-                    (rvalue, "CVRR", "map", None),
-                    (r2value, "CVRR2", "map", None),
-                    (fitcoeff, "CVR", "map", "percent"),
-                ]
         bidsdict = bidsbasedict.copy()
 
         if args.debug or args.focaldebug:

rapidtide/workflows/roisummarize.py

@@ -18,7 +18,6 @@
 #
 import argparse
 import sys
-from argparse import Namespace
 from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
@@ -128,8 +127,8 @@ def _get_parser() -> Any:
 
 
 def summarize4Dbylabel(
-    inputvoxels: Any, templatevoxels: Any, normmethod: str = "z", debug: bool = False
-) -> None:
+    inputvoxels: NDArray, templatevoxels: NDArray, normmethod: str = "z", debug: bool = False
+) -> NDArray:
     """
     Summarize 4D voxel data by region labels from a template.
 
@@ -138,9 +137,9 @@ def summarize4Dbylabel(
 
     Parameters
     ----------
-    inputvoxels : array-like
+    inputvoxels : NDArray
         4D array containing voxel data with shape (n_voxels, n_timepoints, n_other_dims)
-    templatevoxels : array-like
+    templatevoxels : NDArray
         3D array containing region labels with shape (n_voxels, 1, 1)
     normmethod : str, optional
         Normalization method to apply to time courses, default is "z"
@@ -151,7 +150,7 @@ def summarize4Dbylabel(
 
     Returns
     -------
-    timecourses : numpy.ndarray
+    timecourses : NDArray
         2D array of shape (n_regions, n_timepoints) containing normalized mean
         time courses for each region
 
@@ -187,7 +186,9 @@ def summarize4Dbylabel(
     return timecourses
 
 
-def summarize3Dbylabel(inputvoxels: Any, templatevoxels: Any, debug: bool = False) -> None:
+def summarize3Dbylabel(
+    inputvoxels: NDArray, templatevoxels: NDArray, debug: bool = False
+) -> Tuple[NDArray, list]:
     """
     Summarize 3D voxel data by label using mean, standard deviation, and median statistics.
 
@@ -197,9 +198,9 @@ def summarize3Dbylabel(inputvoxels: Any, templatevoxels: Any, debug: bool = Fals
 
     Parameters
     ----------
-    inputvoxels : array-like
+    inputvoxels : NDArray
         3D array containing the voxel values to be summarized
-    templatevoxels : array-like
+    templatevoxels : NDArray
         3D array containing integer labels defining regions of interest
     debug : bool, optional
         Flag to enable debug output (default is False)
@@ -208,7 +209,7 @@ def summarize3Dbylabel(inputvoxels: Any, templatevoxels: Any, debug: bool = Fals
     -------
     tuple
         A tuple containing:
-        - outputvoxels : ndarray
+        - outputvoxels : NDArray
           3D array with each labeled region replaced by its mean value
         - regionstats : list
           List of lists containing [mean, std, median] statistics for each region

rapidtide/workflows/showarbcorr.py

@@ -531,7 +531,7 @@ def showarbcorr(args: Any) -> None:
     print("trimmed Correlator lengths (x, y):", len(xcorr_x_trim), len(thexcorr_trim))
 
     print(f"{len(filtereddata1)=}, {len(filtereddata2)=}")
-    thepxcorr = pearsonr(filtereddata1, filtereddata2)
+    thepxcorr = pearsonr(filtereddata1, filtereddata2).statistic
 
     # initialize the correlation fitter
     thexsimfuncfitter = tide_simFuncClasses.SimilarityFunctionFitter(
@@ -597,7 +597,7 @@ def showarbcorr(args: Any) -> None:
     else:
         # report the pearson correlation
         if showpearson:
-            print("Pearson_R:\t", thepxcorr[0])
+            print("Pearson_R:\t", thepxcorr)
             print("")
         if args.label is not None:
             print(args.label, ":\t", -maxdelay)

rapidtide/workflows/showxcorrx.py

@@ -204,7 +204,7 @@ def _get_parser() -> Any:
         default=False,
     )
 
-    pf.addpermutationopts(preproc, numreps=0)
+    pf.addpermutationopts(parser, numreps=0)
 
     # similarity function options
     similarityopts = parser.add_argument_group("Similarity function options")
@@ -927,7 +927,7 @@ def showxcorrx(args: Any) -> None:
             tide_io.writenpvecs(corrlist_pear, "corrlist_pear.txt")
 
     if args.debug:
-        print(thepxcorr)
+        print(thepxcorr.statistic, thepxcorr.pvalue)
 
     if args.similaritymetric == "mutualinfo":
         print(f"{tcname1}[0] = {tcname2}[{-maxdelaymi} seconds]")
@@ -961,7 +961,7 @@ def showxcorrx(args: Any) -> None:
                     "xcorr_maxdelay",
                 ]
                 thedataitems = [
-                    str(thepxcorr[0]),
+                    str(thepxcorr.statistic),
                     str(pearpcts_fit[0]),
                     str(R),
                     str(pcts_fit[0]),
@@ -970,8 +970,8 @@ def showxcorrx(args: Any) -> None:
             else:
                 thelabelitems = ["pearson_R", "pearson_p", "xcorr_R", "xcorr_maxdelay"]
                 thedataitems = [
-                    str(thepxcorr[0]),
-                    str(thepxcorr[1]),
+                    str(thepxcorr.statistic),
+                    str(thepxcorr.pvalue),
                     str(R),
                     str(-maxdelay),
                 ]
@@ -990,7 +990,7 @@ def showxcorrx(args: Any) -> None:
     """else:
         # report the pearson correlation
         if showpearson:
-            print("Pearson_R:\t", thepxcorr[0])
+            print("Pearson_R:\t", thepxcorr.statistic)
             if args.numestreps > 0:
                 for idx, percentile in enumerate(thepercentiles):
                     print(

rapidtide/workflows/simdata.py

@@ -17,10 +17,10 @@
 #
 #
 import argparse
-from argparse import Namespace
-from typing import Any, Callable, Dict, List, Optional, Tuple, Union
+import sys
+from typing import Any, Optional, Tuple
 
-from matplotlib.pyplot import *
+import numpy as np
 from numpy.typing import NDArray
 
 import rapidtide.filter as tide_filt
@@ -206,7 +206,7 @@ def _get_parser() -> Any:
 
 def prepareband(
     simdatadims: Any,
-    pctfile: Any,
+    pctfile: str,
     sigfracfile: Any,
     lagfile: Any,
     regressorfile: Any,
@@ -228,7 +228,7 @@ def prepareband(
     ----------
     simdatadims : Any
         Spatial dimensions of the fMRI data.
-    pctfile : Any
+    pctfile : str
         Path to the NIfTI file containing percentile data. If None, `sigfracfile` is used.
     sigfracfile : Any
         Path to the NIfTI file containing signal fraction data. Used if `pctfile` is None.
@@ -355,28 +355,28 @@ def prepareband(
 
 
 def fmrisignal(
-    Fs: Any,
-    times: Any,
-    meanvalue: Any,
+    Fs: float,
+    times: NDArray,
+    meanvalue: float,
     dolfo: bool = False,
-    lfowave: Optional[Any] = None,
-    lfomag: Optional[Any] = None,
+    lfowave: Optional[object] = None,
+    lfomag: Optional[NDArray] = None,
     lfodelay: Optional[Any] = None,
     lfonoise: float = 0.0,
-    lfofilter: Optional[Any] = None,
+    lfofilter: Optional[object] = None,
     doresp: bool = False,
-    respwave: Optional[Any] = None,
-    respmag: Optional[Any] = None,
-    respdelay: Optional[Any] = None,
+    respwave: Optional[object] = None,
+    respmag: Optional[NDArray] = None,
+    respdelay: Optional[NDArray] = None,
     respnoise: float = 0.0,
-    respfilter: Optional[Any] = None,
+    respfilter: Optional[object] = None,
     docardiac: bool = False,
-    cardiacwave: Optional[Any] = None,
-    cardiacmag: Optional[Any] = None,
-    cardiacdelay: Optional[Any] = None,
+    cardiacwave: Optional[object] = None,
+    cardiacmag: Optional[NDArray] = None,
+    cardiacdelay: Optional[NDArray] = None,
     cardiacnoise: float = 0.0,
-    cardiacfilter: Optional[Any] = None,
-) -> None:
+    cardiacfilter: Optional[object] = None,
+) -> NDArray:
     """
     Generate an fMRI signal by combining multiple physiological waveforms.
 
@@ -387,15 +387,15 @@ def fmrisignal(
 
     Parameters
     ----------
-    Fs : Any
+    Fs : float
         Sampling frequency of the signal.
-    times : Any
+    times : NDArray
         Time vector for the signal.
-    meanvalue : Any
+    meanvalue : float
         Base mean signal value.
     dolfo : bool, optional
         Whether to include low-frequency oscillation (LFO) component. Default is False.
-    lfowave : Optional[Any], optional
+    lfowave : Optional[object], optional
         Waveform object for LFO signal. Default is None.
     lfomag : Optional[Any], optional
         Magnitude of LFO signal. Default is None.
@@ -403,11 +403,11 @@ def fmrisignal(
         Delay for LFO signal. Default is None.
     lfonoise : float, optional
         Noise level for LFO signal. Default is 0.0.
-    lfofilter : Optional[Any], optional
+    lfofilter : Optional[object], optional
         Filter object for LFO noise. Default is None.
     doresp : bool, optional
         Whether to include respiratory signal component. Default is False.
-    respwave : Optional[Any], optional
+    respwave : Optional[object], optional
         Waveform object for respiratory signal. Default is None.
     respmag : Optional[Any], optional
         Magnitude of respiratory signal. Default is None.
@@ -415,11 +415,11 @@ def fmrisignal(
         Delay for respiratory signal. Default is None.
     respnoise : float, optional
         Noise level for respiratory signal. Default is 0.0.
-    respfilter : Optional[Any], optional
+    respfilter : Optional[object], optional
         Filter object for respiratory noise. Default is None.
     docardiac : bool, optional
         Whether to include cardiac signal component. Default is False.
-    cardiacwave : Optional[Any], optional
+    cardiacwave : Optional[object], optional
         Waveform object for cardiac signal. Default is None.
     cardiacmag : Optional[Any], optional
         Magnitude of cardiac signal. Default is None.
@@ -427,7 +427,7 @@ def fmrisignal(
         Delay for cardiac signal. Default is None.
     cardiacnoise : float, optional
         Noise level for cardiac signal. Default is 0.0.
-    cardiacfilter : Optional[Any], optional
+    cardiacfilter : Optional[object], optional
         Filter object for cardiac noise. Default is None.
 
     Returns
@@ -444,7 +444,6 @@ def fmrisignal(
 
     Examples
     --------
-    >>> import numpy as np
     >>> Fs = 100
     >>> times = np.linspace(0, 10, 1000)
     >>> meanvalue = 1.0
@@ -468,7 +467,8 @@ def fmrisignal(
             cardiacmag * cardiacwave.yfromx(times - cardiacdelay)
             + cardiacnoise * cardiacfilter.apply(Fs, np.random.standard_normal(len(times)))
         )
-    return thesignal + meanvalue
+    thesignal += meanvalue
+    return thesignal
 
 
 def simdata(args: Any) -> None:

rapidtide/workflows/spatialmi.py

@@ -433,7 +433,6 @@ def getMI(
         )
 
 
-
 def spatialmi(args: Any) -> None:
     """
     Compute spatial mutual information (MI) between two 3D images over a specified neighborhood.

rapidtide/workflows/tidepool.py

@@ -3672,7 +3672,9 @@ def updateLUT() -> None:
         timecourse_ax.plot(timeaxis, selected, clear=True)"""
 
 
-def mapwithLUT(theimage: Any, themask: Any, theLUT: Any, dispmin: Any, dispmax: Any) -> None:
+def mapwithLUT(
+    theimage: NDArray, themask: NDArray, theLUT: Any, dispmin: Any, dispmax: Any
+) -> None:
     """
     Map image data using a lookup table with optional masking.
 
@@ -3681,9 +3683,9 @@ def mapwithLUT(theimage: Any, themask: Any, theLUT: Any, dispmin: Any, dispmax:
 
     Parameters
     ----------
-    theimage : array-like
+    theimage : NDArray
         Input image data to be mapped
-    themask : array-like
+    themask : NDArray
         Mask array where values less than 1 will be set to 0 in the output
     theLUT : array-like
         Lookup table array used for mapping
@@ -3694,7 +3696,7 @@ def mapwithLUT(theimage: Any, themask: Any, theLUT: Any, dispmin: Any, dispmax:
 
     Returns
     -------
-    numpy.ndarray
+    NDArray
         Mapped data with shape matching input image, where values are
         mapped using the lookup table and masked according to themask parameter
 

{rapidtide-3.1.dist-info → rapidtide-3.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rapidtide
-Version: 3.1
+Version: 3.1.1
 Summary: Tools for performing correlation analysis on fMRI data.
 Author: Taylor Salo, Daniel M. Drucker, Ph.D., Jeffrey N Stout, Yaroslav O. Halchenko, Derek Monroe
 Author-email: "Blaise deB. Frederick" <blaise.frederick@gmail.com>
@@ -20,29 +20,30 @@ Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
 Classifier: Programming Language :: Python :: 3.13
-Requires-Python: >=3.9
+Requires-Python: >=3.10
 Description-Content-Type: text/x-rst
 License-File: LICENSE
 Requires-Dist: numpy
-Requires-Dist: scipy<=1.15.3
+Requires-Dist: scipy
 Requires-Dist: pandas
 Requires-Dist: pyarrow
 Requires-Dist: scikit-image
 Requires-Dist: scikit-learn
 Requires-Dist: nibabel
 Requires-Dist: nilearn
-Requires-Dist: matplotlib>=3.3.0
-Requires-Dist: pyqtgraph>=0.13.4
+Requires-Dist: matplotlib
+Requires-Dist: pyqtgraph
 Requires-Dist: pyqt6-sip
 Requires-Dist: pyqt6
 Requires-Dist: requests
 Requires-Dist: statsmodels
 Requires-Dist: pywavelets
-Requires-Dist: tensorflow>=2.18.0
-Requires-Dist: tf-keras>=2.18.0
 Requires-Dist: torch
 Requires-Dist: tqdm
 Requires-Dist: versioneer
+Provides-Extra: tf
+Requires-Dist: tensorflow>=2.18.0; extra == "tf"
+Requires-Dist: tf-keras>=2.18.0; extra == "tf"
 Provides-Extra: test
 Requires-Dist: codecov; extra == "test"
 Requires-Dist: coverage; extra == "test"