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

rapidtide/OrthoImageItem.py

@@ -843,11 +843,11 @@ class OrthoImageItem(QtWidgets.QWidget):
 
         Parameters
         ----------
-        theimage : numpy.ndarray
+        theimage : NDArray
             Input image array to be mapped using the lookup table
-        mask : numpy.ndarray
+        mask : NDArray
             Mask array where values less than 1 will be set to transparent (alpha = 0)
-        theLUT : numpy.ndarray
+        theLUT : NDArray
             Lookup table array for color mapping, typically with shape (N, 4) for RGBA values
         dispmin : float
             Minimum display value for scaling the input image
@@ -856,7 +856,7 @@ class OrthoImageItem(QtWidgets.QWidget):
 
         Returns
         -------
-        numpy.ndarray
+        NDArray
             Mapped image array with the same shape as input image, with colors applied
             from the lookup table and masked regions set to transparent
 

rapidtide/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2025-11-08T09:22:00-0500",
+ "date": "2025-11-17T10:45:04-0500",
  "dirty": false,
  "error": null,
- "full-revisionid": "d57dfd2f1902964ec2bdc7a760f361eea22f22aa",
- "version": "3.1"
+ "full-revisionid": "81d19a032c3769c614d87b9bb4d14bcd71cfaf18",
+ "version": "3.1.1"
 }
 '''  # END VERSION_JSON
 

rapidtide/calccoherence.py

@@ -227,15 +227,15 @@ def coherencepass(
 
     Parameters
     ----------
-    fmridata : numpy.ndarray
+    fmridata : NDArray
         Input fMRI data array with shape (time, voxels).
     theCoherer : Any
         Object or function used to perform coherence calculations.
-    coherencefunc : numpy.ndarray
+    coherencefunc : NDArray
         Array to store coherence function results for each voxel.
-    coherencepeakval : numpy.ndarray
+    coherencepeakval : NDArray
         Array to store peak coherence values for each voxel.
-    coherencepeakfreq : numpy.ndarray
+    coherencepeakfreq : NDArray
         Array to store peak coherence frequencies for each voxel.
     alt : bool, optional
         If True, use alternative coherence calculation method. Default is False.

rapidtide/calcnullsimfunc.py

@@ -216,8 +216,7 @@ def getNullDistributionData(
     showprogressbar: bool = True,
     chunksize: int = 1000,
     permutationmethod: str = "shuffle",
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
     debug: bool = False,
 ) -> NDArray:
     """
@@ -249,10 +248,8 @@ def getNullDistributionData(
         Size of chunks for multiprocessing. Default is 1000.
     permutationmethod : str, optional
         Permutation method to use ('shuffle' or other supported methods). Default is 'shuffle'.
-    rt_floatset : type, optional
-        The floating-point type to use for internal calculations. Default is np.float64.
     rt_floattype : str, optional
-        String representation of the floating-point type. Default is 'float64'.
+        String representation of the floating-point type. Default is np.float64.
     debug : bool, optional
         If True, enable debug output. Default is False.
 

rapidtide/calcsimfunc.py

@@ -236,8 +236,7 @@ def correlationpass(
     interptype: str = "univariate",
     showprogressbar: bool = True,
     chunksize: int = 1000,
-    rt_floatset: type = np.float64,
-    rt_floattype: str = "float64",
+    rt_floattype: np.dtype = np.float64,
     debug: bool = False,
 ) -> tuple[int, list[float], NDArray]:
     """
@@ -279,8 +278,6 @@ def correlationpass(
         Whether to display a progress bar. Default is True.
     chunksize : int, optional
         Size of chunks for multiprocessing. Default is 1000.
-    rt_floatset : type, optional
-        Floating-point type for internal computations. Default is np.float64.
     rt_floattype : str, optional
         String representation of floating-point type. Default is 'float64'.
     debug : bool, optional

rapidtide/correlate.py

@@ -253,10 +253,11 @@ def shorttermcorr_1D(
             detrendorder=detrendorder,
             windowfunc=windowfunc,
         )
-        thepcorr = sp.stats.pearsonr(dataseg1, dataseg2)
+        thepearsonresult = sp.stats.pearsonr(dataseg1, dataseg2)
+        thepcorrR, thepcorrp = thepearsonresult.statistic, thepearsonresult.pvalue
         times.append(i * sampletime)
-        corrpertime.append(thepcorr[0])
-        ppertime.append(thepcorr[1])
+        corrpertime.append(thepcorrR)
+        ppertime.append(thepcorrp)
     return (
         np.asarray(times, dtype="float64"),
         np.asarray(corrpertime, dtype="float64"),
@@ -483,50 +484,50 @@ def mutual_info_2d_fast(
     debug: bool = False,
 ) -> float:
     """
-        Compute (normalized) mutual information between two 1D variates from a joint histogram.
+    Compute (normalized) mutual information between two 1D variates from a joint histogram.
 
-        Parameters
-        ----------
-        x : 1D NDArray[np.floating[Any]]
-            First variable.
-        y : 1D NDArray[np.floating[Any]]
-            Second variable.
-        bins : tuple of NDArray
-            Bin edges for the histogram. The first element corresponds to `x` and the second to `y`.
-        sigma : float, optional
-            Sigma for Gaussian smoothing of the joint histogram. Default is 1.
-        normalized : bool, optional
-            If True, compute normalized mutual information as defined in [1]_. Default is True.
-        EPS : float, optional
-            Small constant to avoid numerical errors in logarithms. Default is 1e-6.
-        debug : bool, optional
-            If True, print intermediate values for debugging. Default is False.
+    Parameters
+    ----------
+    x : 1D NDArray[np.floating[Any]]
+        First variable.
+    y : 1D NDArray[np.floating[Any]]
+        Second variable.
+    bins : tuple of NDArray
+        Bin edges for the histogram. The first element corresponds to `x` and the second to `y`.
+    sigma : float, optional
+        Sigma for Gaussian smoothing of the joint histogram. Default is 1.
+    normalized : bool, optional
+        If True, compute normalized mutual information as defined in [1]_. Default is True.
+    EPS : float, optional
+        Small constant to avoid numerical errors in logarithms. Default is 1e-6.
+    debug : bool, optional
+        If True, print intermediate values for debugging. Default is False.
 
-        Returns
-        -------
-        float
-            The computed mutual information (or normalized mutual information if `normalized=True`).
+    Returns
+    -------
+    float
+        The computed mutual information (or normalized mutual information if `normalized=True`).
 
-        Notes
-        -----
-        This function computes mutual information using a 2D histogram and Gaussian smoothing.
-        The normalization follows the approach described in [1]_.
+    Notes
+    -----
+    This function computes mutual information using a 2D histogram and Gaussian smoothing.
+    The normalization follows the approach described in [1]_.
 
-        References
-        ----------
-        .. [1] Colin Studholme, David John Hawkes, Derek L.G. Hill (1998).
-               "Normalized entropy measure for multimodality image alignment".
-               in Proc. Medical Imaging 1998, vol. 3338, San Diego, CA, pp. 132-143.
+    References
+    ----------
+    .. [1] Colin Studholme, David John Hawkes, Derek L.G. Hill (1998).
+           "Normalized entropy measure for multimodality image alignment".
+           in Proc. Medical Imaging 1998, vol. 3338, San Diego, CA, pp. 132-143.
 
-        Examples
-        --------
-        >>> import numpy as np
-        >>> x = np.random.randn(1000)
-        >>> y = np.random.randn(1000)
-        >>> bins = (np.linspace(-3, 3, 64), np.linspace(-3, 3, 64))
-        >>> mi = mutual_info_2d_fast(x, y, bins)
-        >>> print(mi)
-        """
+    Examples
+    --------
+    >>> import numpy as np
+    >>> x = np.random.randn(1000)
+    >>> y = np.random.randn(1000)
+    >>> bins = (np.linspace(-3, 3, 64), np.linspace(-3, 3, 64))
+    >>> mi = mutual_info_2d_fast(x, y, bins)
+    >>> print(mi)
+    """
     xstart = bins[0][0]
     xend = bins[0][-1]
     ystart = bins[1][0]
@@ -552,50 +553,50 @@ def mutual_info_2d(
     debug: bool = False,
 ) -> float:
     """
-        Compute (normalized) mutual information between two 1D variates from a joint histogram.
+    Compute (normalized) mutual information between two 1D variates from a joint histogram.
 
-        Parameters
-        ----------
-        x : 1D NDArray[np.floating[Any]]
-            First variable.
-        y : 1D NDArray[np.floating[Any]]
-            Second variable.
-        bins : tuple of int
-            Number of bins for the histogram. The first element is the number of bins for `x`
-            and the second for `y`.
-        sigma : float, optional
-            Sigma for Gaussian smoothing of the joint histogram. Default is 1.
-        normalized : bool, optional
-            If True, compute normalized mutual information as defined in [1]_. Default is True.
-        EPS : float, optional
-            Small constant to avoid numerical errors in logarithms. Default is 1e-6.
-        debug : bool, optional
-            If True, print intermediate values for debugging. Default is False.
+    Parameters
+    ----------
+    x : 1D NDArray[np.floating[Any]]
+        First variable.
+    y : 1D NDArray[np.floating[Any]]
+        Second variable.
+    bins : tuple of int
+        Number of bins for the histogram. The first element is the number of bins for `x`
+        and the second for `y`.
+    sigma : float, optional
+        Sigma for Gaussian smoothing of the joint histogram. Default is 1.
+    normalized : bool, optional
+        If True, compute normalized mutual information as defined in [1]_. Default is True.
+    EPS : float, optional
+        Small constant to avoid numerical errors in logarithms. Default is 1e-6.
+    debug : bool, optional
+        If True, print intermediate values for debugging. Default is False.
 
-        Returns
-        -------
-        float
-            The computed mutual information (or normalized mutual information if `normalized=True`).
+    Returns
+    -------
+    float
+        The computed mutual information (or normalized mutual information if `normalized=True`).
 
-        Notes
-        -----
-        This function computes mutual information using a 2D histogram and Gaussian smoothing.
-        The normalization follows the approach described in [1]_.
+    Notes
+    -----
+    This function computes mutual information using a 2D histogram and Gaussian smoothing.
+    The normalization follows the approach described in [1]_.
 
-        References
-        ----------
-        .. [1] Colin Studholme, David John Hawkes, Derek L.G. Hill (1998).
-               "Normalized entropy measure for multimodality image alignment".
-               in Proc. Medical Imaging 1998, vol. 3338, San Diego, CA, pp. 132-143.
+    References
+    ----------
+    .. [1] Colin Studholme, David John Hawkes, Derek L.G. Hill (1998).
+           "Normalized entropy measure for multimodality image alignment".
+           in Proc. Medical Imaging 1998, vol. 3338, San Diego, CA, pp. 132-143.
 
-        Examples
-        --------
-        >>> import numpy as np
-        >>> x = np.random.randn(1000)
-        >>> y = np.random.randn(1000)
-        >>> mi = mutual_info_2d(x, y)
-        >>> print(mi)
-        """
+    Examples
+    --------
+    >>> import numpy as np
+    >>> x = np.random.randn(1000)
+    >>> y = np.random.randn(1000)
+    >>> mi = mutual_info_2d(x, y)
+    >>> print(mi)
+    """
     jh, xbins, ybins = np.histogram2d(x, y, bins=bins)
     if debug:
         print(f"{xbins} {ybins}")
@@ -604,60 +605,60 @@ def mutual_info_2d(
 
 
 def proc_MI_histogram(
-        jh: NDArray[np.floating[Any]],
-        sigma: float = 1,
-        normalized: bool = True,
-        EPS: float = 1.0e-6,
-        debug: bool = False,
+    jh: NDArray[np.floating[Any]],
+    sigma: float = 1,
+    normalized: bool = True,
+    EPS: float = 1.0e-6,
+    debug: bool = False,
 ) -> float:
     """
-        Compute the mutual information (MI) between two variables from a joint histogram.
+    Compute the mutual information (MI) between two variables from a joint histogram.
 
-        This function calculates mutual information using the joint histogram of two variables,
-        applying Gaussian smoothing and computing entropy-based MI. It supports both normalized
-        and unnormalized versions of the mutual information.
+    This function calculates mutual information using the joint histogram of two variables,
+    applying Gaussian smoothing and computing entropy-based MI. It supports both normalized
+    and unnormalized versions of the mutual information.
 
-        Parameters
-        ----------
-        jh : ndarray of shape (m, n)
-            Joint histogram of two variables. Should be a 2D array of floating point values.
-        sigma : float, optional
-            Standard deviation for Gaussian smoothing of the joint histogram. Default is 1.0.
-        normalized : bool, optional
-            If True, returns normalized mutual information. If False, returns unnormalized
-            mutual information. Default is True.
-        EPS : float, optional
-            Small constant added to the histogram to avoid numerical issues in log computation.
-            Default is 1e-6.
-        debug : bool, optional
-            If True, prints intermediate values for debugging purposes. Default is False.
+    Parameters
+    ----------
+    jh : ndarray of shape (m, n)
+        Joint histogram of two variables. Should be a 2D array of floating point values.
+    sigma : float, optional
+        Standard deviation for Gaussian smoothing of the joint histogram. Default is 1.0.
+    normalized : bool, optional
+        If True, returns normalized mutual information. If False, returns unnormalized
+        mutual information. Default is True.
+    EPS : float, optional
+        Small constant added to the histogram to avoid numerical issues in log computation.
+        Default is 1e-6.
+    debug : bool, optional
+        If True, prints intermediate values for debugging purposes. Default is False.
 
-        Returns
-        -------
-        float
-            The computed mutual information (MI) between the two variables. The value is
-            positive and indicates the amount of information shared between the variables.
+    Returns
+    -------
+    float
+        The computed mutual information (MI) between the two variables. The value is
+        positive and indicates the amount of information shared between the variables.
 
-        Notes
-        -----
-        The function applies Gaussian smoothing to the joint histogram before computing
-        marginal and joint entropies. The mutual information is computed as:
+    Notes
+    -----
+    The function applies Gaussian smoothing to the joint histogram before computing
+    marginal and joint entropies. The mutual information is computed as:
 
-        .. math::
-            MI = \\frac{H(X) + H(Y)}{H(X,Y)} - 1
+    .. math::
+        MI = \\frac{H(X) + H(Y)}{H(X,Y)} - 1
 
-        where :math:`H(X)`, :math:`H(Y)`, and :math:`H(X,Y)` are the marginal and joint entropies,
-        respectively. If `normalized=False`, the unnormalized MI is returned instead.
+    where :math:`H(X)`, :math:`H(Y)`, and :math:`H(X,Y)` are the marginal and joint entropies,
+    respectively. If `normalized=False`, the unnormalized MI is returned instead.
 
-        Examples
-        --------
-        >>> import numpy as np
-        >>> from scipy import ndimage
-        >>> jh = np.random.rand(10, 10)
-        >>> mi = proc_MI_histogram(jh, sigma=0.5, normalized=True)
-        >>> print(mi)
-        0.123456789
-        """
+    Examples
+    --------
+    >>> import numpy as np
+    >>> from scipy import ndimage
+    >>> jh = np.random.rand(10, 10)
+    >>> mi = proc_MI_histogram(jh, sigma=0.5, normalized=True)
+    >>> print(mi)
+    0.123456789
+    """
 
     # smooth the jh with a gaussian filter of given sigma
     sp.ndimage.gaussian_filter(jh, sigma=sigma, mode="constant", output=jh)
@@ -932,7 +933,9 @@ def mutual_info_to_r(themi: float, d: int = 1) -> float:
 def delayedcorr(
     data1: NDArray, data2: NDArray, delayval: float, timestep: float
 ) -> Tuple[float, float]:
-    return sp.stats.pearsonr(data1, tide_resample.timeshift(data2, delayval / timestep, 30)[0])
+    return sp.stats.pearsonr(
+        data1, tide_resample.timeshift(data2, delayval / timestep, 30).statistic
+    )
 
 
 def cepstraldelay(

rapidtide/data/examples/src/testfmri

@@ -1,5 +1,41 @@
 #!/bin/bash
 
+#rapidtide \
+#    --spatialfilt 2.5 \
+#    --nprocs -1 \
+#    --searchrange -7.5 30 \
+#    --simcalcrange 50 -1 \
+#    --outputlevel more \
+#    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+#    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+#    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+#    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+#    --cleanrefined \
+#    --nofitfilt \
+#    --refinedelayeachpass \
+#    --similaritymetric correlation \
+#    --nonumba \
+#    sub-RAPIDTIDETEST.nii.gz \
+#    ../dst/sub-RAPIDTIDETEST_nonumba
+
+#rapidtide \
+#    --spatialfilt 2.5 \
+#    --nprocs -1 \
+#    --searchrange -7.5 30 \
+#    --simcalcrange 50 -1 \
+#    --outputlevel more \
+#    --graymattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_GRAY \
+#    --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
+#    --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
+#    --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
+#    --cleanrefined \
+#    --nofitfilt \
+#    --refinedelayeachpass \
+#    --similaritymetric correlation \
+#    --spcalculation \
+#    sub-RAPIDTIDETEST.nii.gz \
+#    ../dst/sub-RAPIDTIDETEST_single
+
 rapidtide \
     --spatialfilt 2.5 \
     --nprocs -1 \
@@ -12,13 +48,12 @@ rapidtide \
     --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
     --cleanrefined \
     --nofitfilt \
-    --refinedelayeachpass \
-    --similaritymetric correlation \
-    --nonumba \
+    --focaldebug \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_nonumba
+    ../dst/sub-RAPIDTIDETEST
 
 rapidtide \
+    --CVR \
     --spatialfilt 2.5 \
     --nprocs -1 \
     --searchrange -7.5 30 \
@@ -28,12 +63,9 @@ rapidtide \
     --brainmask sub-RAPIDTIDETEST_brainmask.nii.gz \
     --whitemattermask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_WHITE \
     --csfmask sub-RAPIDTIDETEST_synthseg.nii.gz:SSEG_CSF \
-    --cleanrefined \
-    --nofitfilt \
-    --refinedelayeachpass \
-    --similaritymetric correlation \
+    --regressor ../dst/sub-RAPIDTIDETEST_desc-movingregressor_timeseries.json:pass3 \
     sub-RAPIDTIDETEST.nii.gz \
-    ../dst/sub-RAPIDTIDETEST_numba
+    ../dst/CVRTEST
 
 #rapidtide \
     #--spatialfilt 2.5 \

rapidtide/data/examples/src/testhappy

@@ -95,11 +95,11 @@ happy \
     --usenewvesselmethod \
     --nprocs -1
 
-happy \
-    sub-HAPPYTEST.nii.gz \
-    sub-HAPPYTEST.json \
-    ../dst/happy_tensorflow \
-    --increaseoutputlevel \
-    --usenewvesselmethod \
-    --usetensorflow \
-    --nprocs -1
+#happy \
+#    sub-HAPPYTEST.nii.gz \
+#    sub-HAPPYTEST.json \
+#    ../dst/happy_tensorflow \
+#    --increaseoutputlevel \
+#    --usenewvesselmethod \
+#    --usetensorflow \
+#    --nprocs -1