pyNIBS 0.2024.8__py3-none-any.whl

pynibs/tensor_scaling.py

@@ -0,0 +1,144 @@
+import numpy as np
+import warnings
+
+
+def ellipse_eccentricity( a , b ):
+    """Calculates the eccentricity of an 2D ellipse with the
+    semi axis a and b. An eccentricity of 0 corresponds to a sphere and an
+    eccentricity of 1 means complete eccentric (line) with full restriction to
+    the other axis
+
+    Parameters
+    ----------
+    a : float
+        First semi axis parameter
+    b : float
+        Second semi axis parameter
+
+    Returns
+    -------
+    e : float
+        Eccentricity (0...1)
+    """
+    return np.sqrt(1-(b/a)**2)
+
+
+def rescale_lambda_centerized(D, s, tsc=False):
+    """Rescales the eigenvalues of the matrix D
+    according to their eccentricity. The scale factor is between 0...1 a
+    scale factor of 0.5 would not alter the eigenvalues of the matrix D. A
+    scale factor of 0 would unify all eigenvalues to one value such that it
+    corresponds to a isotropic sphere. A scale factor of 1 alters the
+    eigenvalues in such a way that the resulting ellipsoid is fully
+    eccentric and anisotropic.
+
+    Parameters
+    ----------
+    D : nparray of float
+        (3, 3) Diffusion tensor.
+    s : float
+        Scale parameter [0 (iso) ... 0.5 (unaltered)... 1 (aniso)].
+    tsc : bool
+        Tensor singularity correction.
+
+    Returns
+    -------
+    Ds : np.ndarray of float
+        (3, 3) Scaled diffusion tensor.
+    """
+
+    # print("Tensor scaling factor: " + str(s))
+    # check if tensor matrix contains any element > 0
+    if D.any():
+
+        # reformat data if necessary
+        reformat = 0
+
+        if D.ndim == 1 and D.size == 9:
+            D = np.reshape(D, (3, 3))
+            reformat = 1
+
+        # determine eigenvalues of original diffusion tensor matrix
+        l, v = np.linalg.eig(D)
+        l_idx = np.fliplr(np.argsort(l)[np.newaxis, :])[0]
+        l_idx_reverse = np.argsort(l_idx)
+        l = l[l_idx]
+        v = v[:, l_idx]
+
+        # calculate eccentricity e = [e12, e13, e23]
+        e = ellipse_eccentricity(np.array([l[0], l[0], l[1]]), np.array([l[1], l[2], l[2]]))
+
+        # calculate volume
+        # Vol_old = 4.0/3 * np.pi * L[0]*L[1]*L[2]
+
+        # scale eccentricity
+        if s < 0.5:
+            es = 2.0*e*s
+        elif s > 0.5:
+            es = 2.0*(1-e)*s+2*e-1
+        elif s < 0:
+            raise ValueError('ERROR: scale parameter s must not be smaller than 0!')
+        elif s > 1:
+            raise ValueError('ERROR: scale parameter s must not exceed 1!')
+        elif s == 0.5:
+            es = e
+            warnings.warn('Scale parameter s = 0.5 ... diffusion tensor matrix is unaltered!')
+
+        ls1 = 1
+        ls2 = np.sqrt(1 - es[0]**2)
+        ls3 = np.sqrt(1 - es[1]**2)
+
+        Ls = np.array([ls1, ls2, ls3])
+
+        # calculate scale factor for volume constraint
+        scale = (l[0]*l[1]*l[2])/(Ls[0]*Ls[1]*Ls[2])
+
+        # scale eigenvalues in order to fulfill volume constraint
+        Ls = scale**(1.0/3)*Ls
+
+        # compute scaled diffusion tensor matrix and reorder them
+        Ds = np.dot(np.dot(v[:, l_idx_reverse], np.diag(Ls[l_idx_reverse])), v[:, l_idx_reverse].T)
+
+        # reformat data back again to original format if input was like this
+        if reformat:
+            Ds = np.reshape(Ds, (9), order='F')
+
+    elif tsc:
+        Ds = np.array([1, 0, 0, 0, 1, 0, 0, 0, 1])
+
+    else:
+        Ds = D
+
+    return Ds
+
+
+def rescale_lambda_centerized_workhorse(D, s, tsc=False):
+    """Rescales the eigenvalues of the matrix D
+    according to their eccentricity. The scale factor is between 0...1 a
+    scale factor of 0.5 would not alter the eigenvalues of the matrix D. A
+    scale factor of 0 would unify all eigenvalues to one value such that it
+    corresponds to a isotropic sphere. A scale factor of 1 alters the
+    eigenvalues in such a way that the resulting ellipsoid is fully
+    eccentric and anisotropic
+
+    Parameters
+    ----------
+    D : ndarray of float
+        (n, 9) Diffusion tensor.
+    s : float
+        Scale parameter [0 (iso) ... 0.5 (unaltered)... 1 (aniso)].
+    tsc : bool
+        Tensor singularity correction.
+
+    Returns
+    -------
+    Ds : list of nparray of float
+        (3, 3) Scaled diffusion tensor
+    """
+
+    Ds = np.empty(D.shape)
+
+    for i in range(D.shape[0]):
+        Ds[i, :] = rescale_lambda_centerized(D[i, :], s, tsc)
+
+    return Ds

pynibs/tests/data/InstrumentMarker20200225163611937.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<InstrumentMarkerList coordinateSpace="RAS">
+    <!--All positions are saved in the coordinate system of the corresponding medical data.
+NIfTI image data are recommended using RAS system (x-axis increases from the left hand side to the right hand side of the patient,
+y-axis increases from the posterior side to the anterior side of the patient and z-axis increases from the feet toward the head of the patient).-->
+    <InstrumentMarker alwaysVisible="false" index="0" selected="true">
+        <Marker additionalInformation="" color="#ff0000" description="test" set="true">
+            <Matrix4D data00="0.9013614031176984"
+                data01="0.2983920094889285" data02="-0.3138959024047658"
+                data03="-71.18429093438886" data10="0.38530408399367894"
+                data11="-0.8834528036471245"
+                data12="0.26659466328018544" data13="-79.95375674706612"
+                data20="-0.1977604402582455"
+                data21="-0.3612397546019023"
+                data22="-0.9112724377855788" data23="38.69342634326524"
+                data30="0.0" data31="0.0" data32="0.0" data33="1.0"/>
+        </Marker>
+    </InstrumentMarker>
+</InstrumentMarkerList>

pynibs/tests/data/TriggerMarkers_Coil0_20200225163443682.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<TriggerMarkerList coordinateSpace="RAS" isOnlineReading="false" startTime="16:34:43.636">
+    <!--All positions are saved in the coordinate system of the corresponding medical data.
+NIfTI image data are recommended using RAS system (x-axis increases from the left hand side to the right hand side of the patient,
+y-axis increases from the posterior side to the anterior side of the patient and z-axis increases from the feet toward the head of the patient).-->
+    <ResponseParameters selectedResponseChannel="0">
+        <responseDescription id="response" maxValue="51200.0"
+            minValue="-51200.0" name="Response" unit="uV"/>
+        <responseDescription id="valueA" maxValue="200.0" minValue="0.0"
+            name="Value A (di/dt)" unit="A/us"/>
+        <responseDescription id="amplitudeA" maxValue="100.0"
+            minValue="0.0" name="Amplitude A" unit="%"/>
+    </ResponseParameters>
+</TriggerMarkerList>