rapidtide 3.0.10__py3-none-any.whl → 3.1__py3-none-any.whl

rapidtide/workflows/linfitfilt.py

@@ -18,17 +18,43 @@
 #
 import argparse
 import sys
+from argparse import Namespace
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
+from numpy.typing import NDArray
 
 import rapidtide.fit as tide_fit
 import rapidtide.io as tide_io
 from rapidtide.workflows.parser_funcs import is_valid_file
 
 
-def _get_parser():
+def _get_parser() -> Any:
     """
-    Argument parser for linfitfilt
+    Argument parser for linfitfilt.
+
+    This function constructs and returns an `argparse.ArgumentParser` object configured
+    for the `linfitfilt` command-line tool. It defines all required and optional arguments
+    needed to specify input files, regression parameters, and output options.
+
+    Returns
+    -------
+    argparse.ArgumentParser
+        Configured argument parser for the linfitfilt tool.
+
+    Notes
+    -----
+    The parser is designed to handle:
+    - Input NIfTI files (3D or 4D)
+    - EV (event-related) files for regression
+    - Data masking options
+    - Timecourse skipping for fitting
+    - Output filtering and saving options
+
+    Examples
+    --------
+    >>> parser = _get_parser()
+    >>> args = parser.parse_args()
     """
     parser = argparse.ArgumentParser(
         prog="linfitfilt",
@@ -76,7 +102,67 @@ def _get_parser():
     return parser
 
 
-def linfitfilt(inputfile, numskip, outputroot, evfilename, datamaskname, saveall=True):
+def linfitfilt(
+    inputfile: Any,
+    numskip: Any,
+    outputroot: Any,
+    evfilename: Any,
+    datamaskname: Any,
+    saveall: bool = True,
+) -> None:
+    """
+    Perform linear regression fitting on 4D NIfTI data using specified regressors.
+
+    This function fits a linear model to each voxel's time series using the provided
+    regressors and saves the resulting fit coefficients, R-squared values, and filtered
+    data. It supports both NIfTI and text-based regressor files, as well as FSL par files
+    for global regressors.
+
+    Parameters
+    ----------
+    inputfile : str or pathlib.Path
+        Path to the input 4D NIfTI file containing the time series data.
+    numskip : int
+        Number of initial time points to skip when fitting the model.
+    outputroot : str
+        Root name for output NIfTI files (e.g., '_mean', '_fit0', '_R2', etc.).
+    evfilename : list of str or pathlib.Path
+        List of paths to files containing regressor time series. Can be NIfTI files,
+        text files, or FSL par files.
+    datamaskname : str or pathlib.Path, optional
+        Path to a NIfTI file defining the mask for data analysis. If None, a full mask
+        is assumed.
+    saveall : bool, optional
+        If True, save all intermediate and final output files. Default is True.
+
+    Returns
+    -------
+    None
+        This function does not return a value but saves multiple NIfTI files to disk.
+
+    Notes
+    -----
+    - The function performs ordinary least squares (OLS) regression for each voxel.
+    - The regressors are applied to the data after skipping the first `numskip` time points.
+    - Output files include:
+        - `<outputroot>_mean.nii.gz`: Mean of the data.
+        - `<outputroot>_fit{j}.nii.gz`: Fitted coefficients for regressor j.
+        - `<outputroot>_R2.nii.gz`: R-squared values for the model.
+        - `<outputroot>_totaltoremove.nii.gz`: Regressor contributions to be removed.
+        - `<outputroot>_trimmed.nii.gz`: Trimmed input data.
+        - `<outputroot>_filtered.nii.gz`: Final filtered data.
+
+    Examples
+    --------
+    >>> linfitfilt(
+    ...     inputfile='data.nii.gz',
+    ...     numskip=5,
+    ...     outputroot='output',
+    ...     evfilename=['regressor1.txt', 'regressor2.nii.gz'],
+    ...     datamaskname='mask.nii.gz',
+    ...     saveall=True
+    ... )
+    """
     # initialize some variables
     evdata = []
     evisnifti = []
@@ -238,7 +324,34 @@ def linfitfilt(inputfile, numskip, outputroot, evfilename, datamaskname, saveall
     tide_io.savetonifti(filtereddata, theheader, outputroot + "_filtered")
 
 
-def main():
+def main() -> None:
+    """
+    Main function to execute the linear fit and filter pipeline.
+
+    This function parses command line arguments and executes the linear fit and
+    filter process on the input data file. It handles argument parsing exceptions
+    and provides help output when needed.
+
+    Parameters
+    ----------
+    None
+
+    Returns
+    -------
+    None
+        This function does not return any value.
+
+    Notes
+    -----
+    The function relies on `_get_parser()` to create and return an argument parser
+    with the necessary command line options. The parsed arguments are then passed
+    to the `linfitfilt` function for processing.
+
+    Examples
+    --------
+    >>> main()
+    # Executes the linear fit and filter pipeline with arguments from command line
+    """
     try:
         args = vars(_get_parser().parse_args())
     except SystemExit:

rapidtide/workflows/localflow.py

@@ -19,8 +19,11 @@
 import argparse
 import copy
 import time
+from argparse import Namespace
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import numpy as np
+from numpy.typing import NDArray
 from tqdm import tqdm
 
 import rapidtide.correlate as tide_corr
@@ -41,7 +44,36 @@ DEFAULT_AMPTHRESH = 0.3
 DEFAULT_MINLAGDIFF = 0.0
 
 
-def _get_parser():
+def _get_parser() -> Any:
+    """
+    Create and configure an argument parser for the localflow command-line tool.
+
+    This function sets up an `argparse.ArgumentParser` with a set of predefined
+    command-line arguments used to control the behavior of the local flow analysis
+    pipeline. It includes options for input/output file handling, reconstruction
+    parameters, filtering, windowing, and debugging.
+
+    Returns
+    -------
+    argparse.ArgumentParser
+        Configured argument parser with all required and optional arguments.
+
+    Notes
+    -----
+    The parser includes the following argument groups:
+    - Required positional arguments: `inputfilename` and `outputroot`
+    - Optional arguments for reconstruction parameters such as `npasses`, `radius`,
+      `minlagdiff`, `ampthresh`, `gausssigma`, `oversampfac`, `dofit`, `detrendorder`,
+      and `nosphere`
+    - Miscellaneous options including `noprogressbar` and `debug`
+
+    Examples
+    --------
+    >>> parser = _get_parser()
+    >>> args = parser.parse_args()
+    >>> print(args.inputfilename)
+    'input.nii.gz'
+    """
     # get the command line parameters
     parser = argparse.ArgumentParser(
         prog="localflow",
@@ -149,17 +181,79 @@ def _get_parser():
 
 
 def preprocdata(
-    fmridata,
-    themask,
-    theprefilter,
-    oversamplefactor,
-    Fs,
-    tr,
-    detrendorder=3,
-    windowfunc="hamming",
-    padseconds=0,
-    showprogressbar=True,
-):
+    fmridata: Any,
+    themask: Any,
+    theprefilter: Any,
+    oversamplefactor: Any,
+    Fs: Any,
+    tr: Any,
+    detrendorder: int = 3,
+    windowfunc: str = "hamming",
+    padseconds: int = 0,
+    showprogressbar: bool = True,
+) -> None:
+    """
+    Preprocess fMRI data by resampling, filtering, and normalizing voxel time series.
+
+    This function applies a series of preprocessing steps to fMRI data including:
+    resampling to a higher temporal resolution, applying a filter, and detrending
+    with correlation normalization. It processes each voxel individually based on
+    a provided mask.
+
+    Parameters
+    ----------
+    fmridata : array-like
+        4D fMRI data array with shape (nx, ny, nz, nt), where nx, ny, nz are spatial
+        dimensions and nt is the number of time points.
+    themask : array-like
+        3D binary mask array with the same spatial dimensions as `fmridata`. Voxels
+        with values > 0 are processed.
+    theprefilter : object
+        A filter object with an `apply` method that applies a temporal filter to the data.
+    oversamplefactor : float
+        Factor by which to oversample the data. Must be a positive number.
+    Fs : float
+        Sampling frequency of the original fMRI data in Hz.
+    tr : float
+        Repetition time (TR) of the fMRI acquisition in seconds.
+    detrendorder : int, optional
+        Order of the polynomial used for detrending. Default is 3.
+    windowfunc : str, optional
+        Window function used for correlation normalization. Default is "hamming".
+    padseconds : int, optional
+        Number of seconds to pad the resampled signal. Default is 0.
+    showprogressbar : bool, optional
+        Whether to display a progress bar during voxel processing. Default is True.
+
+    Returns
+    -------
+    tuple
+        A tuple containing:
+        - osfmridata_byvox : ndarray
+            Resampled and filtered fMRI data for processed voxels, shape (numvoxels, ostimepoints).
+        - ostimepoints : int
+            Number of time points in the oversampled data.
+        - oversamptr : float
+            Oversampled repetition time.
+        - numvoxelsprocessed : int
+            Total number of voxels processed.
+
+    Notes
+    -----
+    This function modifies the input data in-place during processing. The output includes
+    only the voxels that are marked as active in `themask`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from some_module import preprocdata
+    >>> fmri_data = np.random.rand(64, 64, 32, 100)
+    >>> mask = np.ones((64, 64, 32))
+    >>> filter_obj = SomeFilter()
+    >>> result = preprocdata(
+    ...     fmri_data, mask, filter_obj, oversamplefactor=2.0, Fs=2.0, tr=2.0
+    ... )
+    """
     numspatiallocs = fmridata.shape[0] * fmridata.shape[1] * fmridata.shape[2]
     timepoints = fmridata.shape[3]
 
@@ -203,19 +297,75 @@ def preprocdata(
 
 
 def getcorrloc(
-    thedata,
-    idx1,
-    idx2,
-    Fs,
-    dofit=False,
-    lagmin=-12.5,
-    lagmax=12.5,
-    widthmax=100.0,
-    negsearch=15.0,
-    possearch=15.0,
-    padding=0,
-    debug=False,
-):
+    thedata: Any,
+    idx1: Any,
+    idx2: Any,
+    Fs: Any,
+    dofit: bool = False,
+    lagmin: float = -12.5,
+    lagmax: float = 12.5,
+    widthmax: float = 100.0,
+    negsearch: float = 15.0,
+    possearch: float = 15.0,
+    padding: int = 0,
+    debug: bool = False,
+) -> None:
+    """
+    Compute the cross-correlation peak between two time series and optionally fit it.
+
+    This function computes the cross-correlation between two time series selected
+    from `thedata` using indices `idx1` and `idx2`. It returns the maximum correlation
+    value, the corresponding time lag, a mask indicating success, and a failure reason.
+
+    Parameters
+    ----------
+    thedata : array_like
+        Input data array of shape (n_channels, n_samples).
+    idx1 : int or array_like
+        Index or indices of the first time series in `thedata`.
+    idx2 : int or array_like
+        Index or indices of the second time series in `thedata`.
+    Fs : float
+        Sampling frequency of the data.
+    dofit : bool, optional
+        If True, perform a peak fit on the cross-correlation function. Default is False.
+    lagmin : float, optional
+        Minimum lag to consider in seconds. Default is -12.5.
+    lagmax : float, optional
+        Maximum lag to consider in seconds. Default is 12.5.
+    widthmax : float, optional
+        Maximum width for fitting. Default is 100.0.
+    negsearch : float, optional
+        Search range for negative lags in seconds. Default is 15.0.
+    possearch : float, optional
+        Search range for positive lags in seconds. Default is 15.0.
+    padding : int, optional
+        Zero-padding for FFT-based correlation. Default is 0.
+    debug : bool, optional
+        If True, print debug information. Default is False.
+
+    Returns
+    -------
+    tuple
+        A tuple of (maxcorr, maxtime, maskval, failreason) where:
+        - maxcorr: Maximum correlation value.
+        - maxtime: Time lag corresponding to maxcorr in seconds.
+        - maskval: Mask indicating fit success (1 = success, 0 = failure).
+        - failreason: Numeric code indicating reason for fit failure (0 = no failure).
+
+    Notes
+    -----
+    - If either time series contains all zeros, the function returns (0.0, 0.0, 0, 0).
+    - The function uses `tide_corr.fastcorrelate` for correlation and `tide_fit.simfuncpeakfit`
+      for fitting when `dofit=True`.
+
+    Examples
+    --------
+    >>> import numpy as np
+    >>> data = np.random.rand(10, 1000)
+    >>> corr, time, mask, reason = getcorrloc(data, 0, 1, Fs=100, dofit=True)
+    >>> print(f"Correlation: {corr}, Lag: {time}s")
+    """
     tc1 = thedata[idx1, :]
     tc2 = thedata[idx2, :]
     if np.any(tc1) != 0.0 and np.any(tc2) != 0.0:
@@ -299,14 +449,90 @@ def getcorrloc(
         return 0.0, 0.0, 0, 0
 
 
-def xyz2index(x, y, z, xsize, ysize, zsize):
+def xyz2index(x: Any, y: Any, z: Any, xsize: Any, ysize: Any, zsize: Any) -> None:
+    """
+    Convert 3D coordinates to a linear index for a 3D array.
+
+    This function maps 3D coordinates (x, y, z) to a linear index assuming
+    row-major order storage of a 3D array with dimensions (xsize, ysize, zsize).
+
+    Parameters
+    ----------
+    x : Any
+        X-coordinate, should be between 0 and xsize-1 inclusive
+    y : Any
+        Y-coordinate, should be between 0 and ysize-1 inclusive
+    z : Any
+        Z-coordinate, should be between 0 and zsize-1 inclusive
+    xsize : Any
+        Size of the array along the x-axis
+    ysize : Any
+        Size of the array along the y-axis
+    zsize : Any
+        Size of the array along the z-axis
+
+    Returns
+    -------
+    int
+        Linear index if coordinates are valid (within bounds), -1 otherwise
+
+    Notes
+    -----
+    The function uses row-major order indexing: index = z + y * zsize + x * zsize * ysize
+
+    Examples
+    --------
+    >>> xyz2index(1, 2, 3, 10, 10, 10)
+    321
+    >>> xyz2index(15, 2, 3, 10, 10, 10)
+    -1
+    """
     if (0 <= x < xsize) and (0 <= y < ysize) and (0 <= z < zsize):
         return int(z) + int(y) * int(zsize) + int(x) * int(zsize * ysize)
     else:
         return -1
 
 
-def index2xyz(theindex, ysize, zsize):
+def index2xyz(theindex: Any, ysize: Any, zsize: Any) -> None:
+    """
+    Convert a linear index to 3D coordinates (x, y, z).
+
+    This function maps a 1D index to 3D coordinates within a 3D grid
+    with dimensions determined by ysize and zsize. The conversion assumes
+    row-major ordering where the index is distributed across the three
+    dimensions based on the product of the grid dimensions.
+
+    Parameters
+    ----------
+    theindex : Any
+        The linear index to be converted to 3D coordinates
+    ysize : Any
+        The size of the grid in the y dimension
+    zsize : Any
+        The size of the grid in the z dimension
+
+    Returns
+    -------
+    tuple
+        A tuple containing (x, y, z) coordinates corresponding to the input index
+
+    Notes
+    -----
+    The function assumes that the grid dimensions are such that the total
+    number of elements is sufficient to accommodate the given index.
+    The conversion follows the formula:
+    - x = index // (ysize * zsize)
+    - y = (index - x * ysize * zsize) // zsize
+    - z = index - x * ysize * zsize - y * zsize
+
+    Examples
+    --------
+    >>> index2xyz(10, 3, 4)
+    (0, 0, 10)
+
+    >>> index2xyz(25, 3, 4)
+    (2, 0, 1)
+    """
     x = theindex // int(zsize * ysize)
     theindex -= int(x) * int(zsize * ysize)
     y = theindex // int(zsize)
@@ -315,7 +541,81 @@ def index2xyz(theindex, ysize, zsize):
     return x, y, z
 
 
-def localflow(args):
+def localflow(args: Any) -> None:
+    """
+    Perform local flow analysis on fMRI data.
+
+    This function processes fMRI data to compute local correlation and delay information
+    across spatial neighbors, followed by a reconstruction step to estimate time delays
+    in the signal propagation.
+
+    Parameters
+    ----------
+    args : Any
+        An object containing various arguments for processing, including:
+        - inputfilename : str
+            Path to the input NIfTI file.
+        - outputroot : str
+            Root name for output files.
+        - gausssigma : float
+            Sigma for Gaussian spatial smoothing. If less than 0, automatically computed.
+        - oversampfactor : int
+            Oversampling factor for preprocessing. If -1, computed automatically.
+        - detrendorder : int
+            Order of detrending to apply.
+        - windowfunc : str
+            Window function to use for preprocessing.
+        - padseconds : float
+            Padding in seconds for preprocessing.
+        - showprogressbar : bool
+            Whether to show progress bars.
+        - dofit : bool
+            Whether to fit the correlation.
+        - debug : bool
+            Whether to enable debug mode.
+        - radius : float
+            Neighborhood radius in mm.
+        - npasses : int
+            Number of reconstruction passes.
+        - ampthresh : float
+            Amplitude threshold for valid correlations.
+
+    Returns
+    -------
+    None
+        This function does not return a value but saves multiple NIfTI files and timing logs.
+
+    Notes
+    -----
+    The function performs the following steps:
+    1. Reads and preprocesses input fMRI data.
+    2. Applies spatial filtering if specified.
+    3. Prepares data for correlation analysis.
+    4. Identifies spatial neighbors within a specified radius.
+    5. Computes local correlations and delays.
+    6. Reconstructs time delays using iterative averaging.
+    7. Saves results as NIfTI files.
+
+    Examples
+    --------
+    >>> import argparse
+    >>> args = argparse.Namespace(
+    ...     inputfilename="fmri.nii.gz",
+    ...     outputroot="output",
+    ...     gausssigma=-1.0,
+    ...     oversampfactor=-1,
+    ...     detrendorder=1,
+    ...     windowfunc="hann",
+    ...     padseconds=10.0,
+    ...     showprogressbar=True,
+    ...     dofit=True,
+    ...     debug=False,
+    ...     radius=5.0,
+    ...     npasses=5,
+    ...     ampthresh=0.1
+    ... )
+    >>> localflow(args)
+    """
     # set default variable values
     displayplots = False
 

rapidtide/workflows/mergequality.py

@@ -17,6 +17,8 @@
 #
 #
 import argparse
+from argparse import Namespace
+from typing import Any, Callable, Dict, List, Optional, Tuple, Union
 
 import pandas as pd
 
@@ -24,9 +26,29 @@ import rapidtide.io as tide_io
 import rapidtide.stats as tide_stats
 
 
-def _get_parser():
+def _get_parser() -> Any:
     """
-    Argument parser for mergequality
+    Argument parser for mergequality.
+
+    Creates and configures an argument parser for the mergequality tool that merges
+    rapidtide quality check data from multiple runs.
+
+    Returns
+    -------
+    argparse.ArgumentParser
+        Configured argument parser object with all required and optional arguments
+        for the mergequality tool.
+
+    Notes
+    -----
+    The returned parser is configured with:
+    - Required arguments: --input and --outputroot
+    - Optional arguments: --keyfile, --showhists, --addgraymetrics, --addwhitemetrics, --debug
+
+    Examples
+    --------
+    >>> parser = _get_parser()
+    >>> args = parser.parse_args(['--input', 'run1.csv', 'run2.csv', '--outputroot', 'merged'])
     """
     parser = argparse.ArgumentParser(
         prog="mergequality",
@@ -68,7 +90,61 @@ def _get_parser():
     return parser
 
 
-def mergequality(args):
+def mergequality(args: Any) -> None:
+    """
+    Merge quality metrics from multiple input JSON files into a single CSV file.
+
+    This function reads quality metrics from input JSON files and combines them
+    into a structured DataFrame. It supports optional inclusion of gray and white
+    matter specific metrics based on command-line arguments. Histograms for each
+    metric are also generated and saved.
+
+    Parameters
+    ----------
+    args : Any
+        An object containing the following attributes:
+        - input : list of str
+            List of input JSON file paths to process.
+        - outputroot : str
+            Base name for output CSV and histogram files.
+        - keyfile : str, optional
+            Path to a JSON file containing key metrics definitions. If None,
+            default metrics are used.
+        - addgraymetrics : bool
+            Whether to include gray matter specific metrics.
+        - addwhitemetrics : bool
+            Whether to include white matter specific metrics.
+        - showhists : bool
+            Whether to display histograms.
+        - debug : bool
+            Whether to print debug information.
+
+    Returns
+    -------
+    None
+        This function does not return a value but saves a CSV file and histogram
+        plots to disk.
+
+    Notes
+    -----
+    The function uses `tide_io.readdictfromjson` to read input JSON files and
+    `tide_stats.makeandsavehistogram` to generate histograms. Default metrics
+    are included for mask, regressor, lag, laggrad, strength, and MTT.
+    Gray and white matter metrics are conditionally added based on `args`.
+
+    Examples
+    --------
+    >>> args = type('Args', (), {
+    ...     'input': ['file1.json', 'file2.json'],
+    ...     'outputroot': 'output',
+    ...     'keyfile': None,
+    ...     'addgraymetrics': True,
+    ...     'addwhitemetrics': False,
+    ...     'showhists': True,
+    ...     'debug': False
+    ... })()
+    >>> mergequality(args)
+    """
     if args.debug:
         print(f"{args.input=}")
         print(f"{args.outputroot=}")