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muscbridge · Sep 10, 2024 · ce158a4 · ce158a4
1 parent d48ac50
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diff --git a/pydesigner/Tensor_Fit_Guide.ipynb b/pydesigner/Tensor_Fit_Guide.ipynb
@@ -24,12 +24,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import nibabel as nib\n",
-    "import numpy as np\n",
-    "from fitting import dwipy as dp \n",
+    "import os\n",
+    "\n",
     "import matplotlib.pyplot as plt\n",
-    "import time\n",
-    "import os"
+    "from fitting import dwipy as dp"
    ]
   },
   {
@@ -49,8 +47,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "niiPath = '/Users/sid/Downloads/MUS_C_001/out/preprocessed_dwi.nii'\n",
-    "savePath = '/Users/sid/Downloads/MUS_C_001/out/expit2'"
+    "niiPath = \"/Users/sid/Downloads/MUS_C_001/out/preprocessed_dwi.nii\"\n",
+    "savePath = \"/Users/sid/Downloads/MUS_C_001/out/expit2\""
    ]
   },
   {
@@ -133,19 +131,19 @@
     }
    ],
    "source": [
-    "fig = plt.figure(figsize=(18, 16), dpi= 80)\n",
-    "img1 = fig.add_subplot(1,3,1)\n",
-    "img1.imshow(myimage.img[:,:,30,0])    # Plot first volume, slice 30 (B0)\n",
-    "img1.title.set_text('B0')\n",
-    "img1.axis('off')\n",
-    "img2 = fig.add_subplot(1,3,2)\n",
-    "img2.imshow(myimage.img[:,:,30,10])   # Plot 10th volume, slice 30 (B1000)\n",
-    "img2.title.set_text('B1000')\n",
-    "img2.axis('off')\n",
-    "img3 = fig.add_subplot(1,3,3)\n",
-    "img3.imshow(myimage.img[:,:,30,60])  # Plot 70th volume, slice 30 (B2000)\n",
-    "img3.title.set_text('B2000')\n",
-    "img3.axis('off')"
+    "fig = plt.figure(figsize=(18, 16), dpi=80)\n",
+    "img1 = fig.add_subplot(1, 3, 1)\n",
+    "img1.imshow(myimage.img[:, :, 30, 0])  # Plot first volume, slice 30 (B0)\n",
+    "img1.title.set_text(\"B0\")\n",
+    "img1.axis(\"off\")\n",
+    "img2 = fig.add_subplot(1, 3, 2)\n",
+    "img2.imshow(myimage.img[:, :, 30, 10])  # Plot 10th volume, slice 30 (B1000)\n",
+    "img2.title.set_text(\"B1000\")\n",
+    "img2.axis(\"off\")\n",
+    "img3 = fig.add_subplot(1, 3, 3)\n",
+    "img3.imshow(myimage.img[:, :, 30, 60])  # Plot 70th volume, slice 30 (B2000)\n",
+    "img3.title.set_text(\"B2000\")\n",
+    "img3.axis(\"off\")"
    ]
   },
   {
@@ -185,7 +183,7 @@
     }
    ],
    "source": [
-    "outliers, dt_est = myimage.irlls()    # Produce 4D outlier map"
+    "outliers, dt_est = myimage.irlls()  # Produce 4D outlier map"
    ]
   },
   {
@@ -225,19 +223,19 @@
     }
    ],
    "source": [
-    "fig = plt.figure(figsize=(18, 16), dpi= 80)\n",
-    "img1 = fig.add_subplot(1,3,1)\n",
-    "img1.imshow(outliers[:,:,30,0])       # Plot first volume, slice 30 (B0)\n",
-    "img1.title.set_text('B0')\n",
-    "img1.axis('off')\n",
-    "img2 = fig.add_subplot(1,3,2)\n",
-    "img2.imshow(outliers[:,:,30,10])      # Plot 10th volume, slice 30 (B1000)\n",
-    "img2.title.set_text('B1000')\n",
-    "img2.axis('off')\n",
-    "img3 = fig.add_subplot(1,3,3)\n",
-    "img3.imshow(outliers[:,:,30,60])     # Plot 100th volume, slice 30 (B2000)\n",
-    "img3.title.set_text('B2000')\n",
-    "img3.axis('off')"
+    "fig = plt.figure(figsize=(18, 16), dpi=80)\n",
+    "img1 = fig.add_subplot(1, 3, 1)\n",
+    "img1.imshow(outliers[:, :, 30, 0])  # Plot first volume, slice 30 (B0)\n",
+    "img1.title.set_text(\"B0\")\n",
+    "img1.axis(\"off\")\n",
+    "img2 = fig.add_subplot(1, 3, 2)\n",
+    "img2.imshow(outliers[:, :, 30, 10])  # Plot 10th volume, slice 30 (B1000)\n",
+    "img2.title.set_text(\"B1000\")\n",
+    "img2.axis(\"off\")\n",
+    "img3 = fig.add_subplot(1, 3, 3)\n",
+    "img3.imshow(outliers[:, :, 30, 60])  # Plot 100th volume, slice 30 (B2000)\n",
+    "img3.title.set_text(\"B2000\")\n",
+    "img3.axis(\"off\")"
    ]
   },
   {
@@ -273,7 +271,7 @@
     }
    ],
    "source": [
-    "myimage.fit(constraints=[0,1,0])"
+    "myimage.fit(constraints=[0, 1, 0])"
    ]
   },
   {
@@ -346,22 +344,22 @@
     }
    ],
    "source": [
-    "print('This is a ' + myimage.tensorType().upper() + ' image')\n",
+    "print(\"This is a \" + myimage.tensorType().upper() + \" image\")\n",
     "\n",
     "DT, KT = myimage.tensorReorder(myimage.tensorType())\n",
     "\n",
-    "print('Shape of DT tensor is ' + str(DT.shape))\n",
-    "print('Shape of KT tensor is ' + str(KT.shape))\n",
+    "print(\"Shape of DT tensor is \" + str(DT.shape))\n",
+    "print(\"Shape of KT tensor is \" + str(KT.shape))\n",
     "\n",
-    "fig = plt.figure(figsize=(18, 16), dpi= 80)\n",
-    "img1 = fig.add_subplot(1,2,1)\n",
-    "img1.imshow(DT[:,:,30,1]) \n",
-    "img1.title.set_text('DT 2 2')\n",
-    "img1.axis('off')\n",
-    "img2 = fig.add_subplot(1,2,2)\n",
-    "img2.imshow(KT[:,:,30, 7])   \n",
-    "img2.title.set_text('K  2 2 2 2')\n",
-    "img2.axis('off')"
+    "fig = plt.figure(figsize=(18, 16), dpi=80)\n",
+    "img1 = fig.add_subplot(1, 2, 1)\n",
+    "img1.imshow(DT[:, :, 30, 1])\n",
+    "img1.title.set_text(\"DT 2 2\")\n",
+    "img1.axis(\"off\")\n",
+    "img2 = fig.add_subplot(1, 2, 2)\n",
+    "img2.imshow(KT[:, :, 30, 7])\n",
+    "img2.title.set_text(\"K  2 2 2 2\")\n",
+    "img2.axis(\"off\")"
    ]
   },
   {
@@ -421,7 +419,7 @@
     }
    ],
    "source": [
-    "myimage.akccorrect(akc_out=akc_out, window=7, connectivity='all')\n",
+    "myimage.akccorrect(akc_out=akc_out, window=7, connectivity=\"all\")\n",
     "mk, rk, ak, kfa, mkt, trace = myimage.extractDKI()"
    ]
   },
@@ -449,28 +447,28 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mdPath = os.path.join(savePath, 'MD.nii')\n",
-    "rdPath = os.path.join(savePath, 'RD.nii')\n",
-    "adPath = os.path.join(savePath, 'AD.nii')\n",
-    "faPath = os.path.join(savePath, 'FA.nii')\n",
-    "fePath = os.path.join(savePath, 'FE.nii')\n",
-    "tracePath = os.path.join(savePath, 'Trace.nii')\n",
-    "mkPath = os.path.join(savePath, 'MK.nii')\n",
-    "rkPath = os.path.join(savePath, 'RK.nii')\n",
-    "akPath = os.path.join(savePath, 'AK.nii')\n",
-    "outlierPath = os.path.join(savePath, 'Outliers_IRLLS.nii')\n",
-    "akcPath = os.path.join(savePath, 'Outliers_AKC.nii')\n",
-    "kfaPath = akPath = os.path.join(savePath, 'KFA.nii')\n",
-    "mktPath = os.path.join(savePath, 'MKT.nii')\n",
-    "dtPath = os.path.join(savePath, 'DT.nii')\n",
-    "ktPath = os.path.join(savePath, 'KT.nii')\n",
-    "awfPath = os.path.join(savePath, 'wmti_awf.nii')\n",
-    "easadPath = os.path.join(savePath, 'wmti_eas_ad.nii')\n",
-    "easrdPath = os.path.join(savePath, 'wmti_eas_rd.nii')\n",
-    "eastortPath = os.path.join(savePath, 'wmti_eas_tort.nii')\n",
-    "iasadPath = os.path.join(savePath, 'wmti_ias_ad.nii')\n",
-    "iasrdPath = os.path.join(savePath, 'wmti_ias_rd.nii')\n",
-    "iastortPath = os.path.join(savePath, 'wmti_ias_tort.nii')\n",
+    "mdPath = os.path.join(savePath, \"MD.nii\")\n",
+    "rdPath = os.path.join(savePath, \"RD.nii\")\n",
+    "adPath = os.path.join(savePath, \"AD.nii\")\n",
+    "faPath = os.path.join(savePath, \"FA.nii\")\n",
+    "fePath = os.path.join(savePath, \"FE.nii\")\n",
+    "tracePath = os.path.join(savePath, \"Trace.nii\")\n",
+    "mkPath = os.path.join(savePath, \"MK.nii\")\n",
+    "rkPath = os.path.join(savePath, \"RK.nii\")\n",
+    "akPath = os.path.join(savePath, \"AK.nii\")\n",
+    "outlierPath = os.path.join(savePath, \"Outliers_IRLLS.nii\")\n",
+    "akcPath = os.path.join(savePath, \"Outliers_AKC.nii\")\n",
+    "kfaPath = akPath = os.path.join(savePath, \"KFA.nii\")\n",
+    "mktPath = os.path.join(savePath, \"MKT.nii\")\n",
+    "dtPath = os.path.join(savePath, \"DT.nii\")\n",
+    "ktPath = os.path.join(savePath, \"KT.nii\")\n",
+    "awfPath = os.path.join(savePath, \"wmti_awf.nii\")\n",
+    "easadPath = os.path.join(savePath, \"wmti_eas_ad.nii\")\n",
+    "easrdPath = os.path.join(savePath, \"wmti_eas_rd.nii\")\n",
+    "eastortPath = os.path.join(savePath, \"wmti_eas_tort.nii\")\n",
+    "iasadPath = os.path.join(savePath, \"wmti_ias_ad.nii\")\n",
+    "iasrdPath = os.path.join(savePath, \"wmti_ias_rd.nii\")\n",
+    "iastortPath = os.path.join(savePath, \"wmti_ias_tort.nii\")\n",
     "dp.writeNii(md, myimage.hdr, mdPath)\n",
     "dp.writeNii(rd, myimage.hdr, rdPath)\n",
     "dp.writeNii(ad, myimage.hdr, adPath)\n",
@@ -568,15 +566,15 @@
    "source": [
     "# fig = plt.figure(figsize=(18, 16), dpi= 80)\n",
     "# img1 = fig.add_subplot(1,3,1)\n",
-    "# img1.imshow(fa[:,:,30]) \n",
+    "# img1.imshow(fa[:,:,30])\n",
     "# img1.title.set_text('FA')\n",
     "# img1.axis('off')\n",
     "# img2 = fig.add_subplot(1,3,2)\n",
-    "# img2.imshow(md[:,:,30])   \n",
+    "# img2.imshow(md[:,:,30])\n",
     "# img2.title.set_text('MD')\n",
     "# img2.axis('off')\n",
     "# img3 = fig.add_subplot(1,3,3)\n",
-    "# img3.imshow(mk_clipped[:,:,30])     \n",
+    "# img3.imshow(mk_clipped[:,:,30])\n",
     "# img3.title.set_text('MK')\n",
     "# img3.axis('off')"
    ]

diff --git a/pydesigner/fitting/dwipy.py b/pydesigner/fitting/dwipy.py
@@ -1099,11 +1099,7 @@ def extractDTI(
         md = (l1 + l2 + l3) / 3
         rd = (l2 + l3) / 2
         ad = l1
-        fa = (
-            np.sqrt(1 / 2)
-            * np.sqrt((l1 - l2) ** 2 + (l2 - l3) ** 2 + (l3 - l1) ** 2)
-            / np.sqrt(l1**2 + l2**2 + l3**2)
-        )
+        fa = np.sqrt(1 / 2) * np.sqrt((l1 - l2) ** 2 + (l2 - l3) ** 2 + (l3 - l1) ** 2) / np.sqrt(l1**2 + l2**2 + l3**2)
         fe = np.abs(np.stack((fa * v1[:, :, :, 0], fa * v1[:, :, :, 1], fa * v1[:, :, :, 2]), axis=3))
         trace = vectorize(trace.T, self.mask)
         return md, rd, ad, fa, fe, trace
@@ -1370,9 +1366,7 @@ def __costCalculator(grid, BT, GT, b0, IMG, iDT, iaDT, zeta, shB, Pl0, g2l_fa_R_
                                 (-BT[b] * (1 - awf) ** -1)
                                 * np.diag((GT[b].dot((iDT - (awf**3 * zeta**-2) * iaDT).dot(GT[b].T))))
                             )
-                        ) * (
-                            1 - awf
-                        )  # Eq. 3 FBWM paper
+                        ) * (1 - awf)  # Eq. 3 FBWM paper
                         Sa = (2 * np.pi * b0 * zeta * np.sqrt(np.pi / BT[b])) * (
                             shB[b].dot((Pl0 * g2l_fa_R_b[b, idx, :][0] * clm))
                         )  # Eq. 4 FBM paper
@@ -1557,8 +1551,7 @@ def fbi_helper(
                                 gamma((l_num + 1) / 2 + int_grid)
                                 * gamma(l_num + (3 / 2))
                                 * (
-                                    (-BT[b] * f_grid[idx_hyper] ** 2 * zeta**-2)
-                                    * np.ones((1, len(f_grid[idx_hyper])))
+                                    (-BT[b] * f_grid[idx_hyper] ** 2 * zeta**-2) * np.ones((1, len(f_grid[idx_hyper])))
                                 ).T
                                 ** int_grid
                                 / (factorial(int_grid) * gamma(l_num + (3 / 2) + int_grid) * gamma((l_num + 1) / 2))
@@ -1580,11 +1573,7 @@ def fbi_helper(
                     idx_Y = 0
                     for l_num in degs[::2]:
                         g2l_fa_R_large[idx_Y : idx_Y + (2 * l_num + 1), np.squeeze(~idx_hyper)] = npm.repmat(
-                            (
-                                np.exp(
-                                    -l_num // 2 * (l_num + 1) / ((2 * BT[b] * (f_grid[~idx_hyper] ** 2 * zeta**-2)))
-                                )
-                            ),
+                            (np.exp(-l_num // 2 * (l_num + 1) / (2 * BT[b] * (f_grid[~idx_hyper] ** 2 * zeta**-2)))),
                             (2 * l_num + 1),
                             1,
                         )  # Eq. 20 FBI paper
@@ -1887,7 +1876,13 @@ def fbi_helper(
 
     def extractWMTI(
         self,
-    ) -> Tuple[np.ndarray[float], np.ndarray[float], np.ndarray[float], np.ndarray[float], np.ndarray[float],]:
+    ) -> Tuple[
+        np.ndarray[float],
+        np.ndarray[float],
+        np.ndarray[float],
+        np.ndarray[float],
+        np.ndarray[float],
+    ]:
         """Returns white matter tract integrity (WMTI) parameters. Warning:
         this can only be run after fitting and DWI.extractDTI().
 
@@ -2167,8 +2162,9 @@ def akccorrect(self, akc_out: np.ndarray[bool], window: int = 3, connectivity: s
                         connLimit = 24
                 else:
                     raise Exception(
-                        'Connectivity choice "{}" is invalid. Please '
-                        'enter either "all" or "face".'.format(connectivity)
+                        'Connectivity choice "{}" is invalid. Please ' 'enter either "all" or "face".'.format(
+                            connectivity
+                        )
                     )
                 nVoil = np.sum(patchViol)
 

diff --git a/pydesigner/main.py b/pydesigner/main.py
@@ -1,5 +1,4 @@
-"""Runs the PyDesigner pipeline
-"""
+"""Runs the PyDesigner pipeline"""
 
 import argparse  # ArgumentParser, add_argument
 import glob  # recursive file search
@@ -916,9 +915,9 @@ def main():
             os.rename(mif_smoothing, working_path)
             # update command history
             cmdtable["smooth"] = [
-                "designer.preprocessing.mrpreproc.smooth(input={}, "
-                "output={}, "
-                "fwhm={}".format(working_path, mif_smoothing, args.fwhm)
+                "designer.preprocessing.mrpreproc.smooth(input={}, " "output={}, " "fwhm={}".format(
+                    working_path, mif_smoothing, args.fwhm
+                )
             ]
             cmdtable["smooth"].append(mrinfoutil.commandhistory(working_path)[-1])
             cmdtable["HEAD"] = cmdtable["smooth"]
@@ -957,10 +956,9 @@ def main():
             os.rename(mif_rician, working_path)
             # update command history
             cmdtable["rician"] = [
-                "designer.preprocessing.mrpreproc."
-                "riciancorrect(input={}, "
-                "output={}, "
-                "noise={})".format(working_path, mif_rician, filetable["noisemap"].getFull())
+                "designer.preprocessing.mrpreproc." "riciancorrect(input={}, " "output={}, " "noise={})".format(
+                    working_path, mif_rician, filetable["noisemap"].getFull()
+                )
             ]
             cmdtable["rician"].append(mrinfoutil.commandhistory(working_path)[-1])
             cmdtable["HEAD"] = cmdtable["rician"]

diff --git a/pydesigner/postprocessing/filters.py b/pydesigner/postprocessing/filters.py
@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 # -*- coding : utf-8 -*-
 
-"""This module contains filter(s) for postprocessing DTI/DKI maps
-"""
+"""This module contains filter(s) for postprocessing DTI/DKI maps"""
 
 # ---------------------------------------------------------------------
 # Package Management

diff --git a/pydesigner/preprocessing/mrpreproc.py b/pydesigner/preprocessing/mrpreproc.py
@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 # -*- coding : utf-8 -*-
 
-"""Utilities for running various MRtrix3's DWI preprocessing tools
-"""
+"""Utilities for running various MRtrix3's DWI preprocessing tools"""
 
 import os
 import os.path as op

diff --git a/pydesigner/preprocessing/preparation.py b/pydesigner/preprocessing/preparation.py
@@ -1,8 +1,7 @@
 #!/usr/bin/env python
 # -*- coding : utf-8 -*-
 
-"""Adds utilities for preparing the data for eddy and analysis
-"""
+"""Adds utilities for preparing the data for eddy and analysis"""
 
 import os  # mkdir
 import os.path as op  # dirname, basename, join, splitext

diff --git a/pydesigner/preprocessing/util.py b/pydesigner/preprocessing/util.py
@@ -1,5 +1,4 @@
-"""Adds utilities for the command-line interface
-"""
+"""Adds utilities for the command-line interface"""
 
 import json  # decode
 import os