changeset 0:94f6b3e28c36 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dmri.py	Fri Nov 03 08:52:47 2017 -0400
@@ -0,0 +1,51 @@
+#!/usr/bin/env python
+import argparse
+import os
+import nibabel
+import shutil
+
+from dipy.data import fetch_sherbrooke_3shell
+
+parser = argparse.ArgumentParser()
+parser.add_argument('--input', dest='input', help='Input dataset')
+parser.add_argument('--output', dest='output', help='Output dataset')
+
+args = parser.parse_args()
+
+def move_directory_files(source_dir, destination_dir, copy=False, remove_source_dir=False):
+    source_directory = os.path.abspath(source_dir)
+    destination_directory = os.path.abspath(destination_dir)
+    if not os.path.isdir(destination_directory):
+        os.makedirs(destination_directory)
+    for dir_entry in os.listdir(source_directory):
+        source_entry = os.path.join(source_directory, dir_entry)
+        if copy:
+            shutil.copy(source_entry, destination_directory)
+        else:
+            shutil.move(source_entry, destination_directory)
+    if remove_source_dir:
+        os.rmdir(source_directory)
+
+input_dir = 'input_dir'
+# Get input data.
+fetch_sherbrooke_3shell()
+# MNove inputs to working directory.
+move_directory_files('/home/greg/.dipy', input_dir)
+fdwi = join(input_dir, 'HARDI193.nii.gz')
+fbval = join(input_dir, 'HARDI193.bval')
+fbvec = join(input_dir, 'HARDI193.bvec')
+# Load the dMRI datasets.
+img = nibabel.load(fdwi)
+data = img.get_data()
+# data is a 4D array where the first 3 dimensions are the i, j,
+# k voxel coordinates and the last dimension is the number of
+# non-weighted (S0s) and diffusion-weighted volumes.
+# Visualize the results using matplotlib.
+axial_middle = data.shape[2] // 2
+plt.figure('Showing the datasets')
+plt.subplot(1, 2, 1).set_axis_off()
+plt.imshow(data[:, :, axial_middle, 0].T, cmap='gray', origin='lower')
+plt.subplot(1, 2, 2).set_axis_off()
+plt.imshow(data[:, :, axial_middle, 10].T, cmap='gray', origin='lower')
+plt.show()
+plt.savefig(args.output, bbox_inches='tight')

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dmri.xml	Fri Nov 03 08:52:47 2017 -0400
@@ -0,0 +1,33 @@
+<tool id="dmri" name="dMRI" version="0.13.0">
+    <description>real-time object detection</description>
+    <requirements>
+        <requirement type="package" version="0.13.0">dipy</requirement>
+        <requirement type="package" version="2.2.0">nibabel</requirement>
+        <requirement type="package" version="2.1.0">matplotlib</requirement>
+    </requirements>
+    <command detect_errors="exit_code"><![CDATA[
+python '$__tool_directory__/drmi.py'
+--input '$input'
+--output '$output'
+    ]]></command>
+    <inputs>
+        <param name="input" format="nifti1" type="data" label="Image"/>
+    </inputs>
+    <outputs>
+        <data name="output_shape_confidence" format="png" />
+    </outputs>
+    <tests>
+        <test>
+        </test>
+    </tests>
+    <help>
+**What it does**
+
+-----
+
+**Options**
+
+    </help>
+    <citations>
+    </citations>
+</tool>