Merge pull request #293 from Eric89GXL/remove-trace

FIX: Remove trace by default

Allows for discarding the trace, and making it the default behavior. It generally seems to be nuisance (non-)data in the analysis process.

Add appveyor build and badge.

Author: matthew-brett

README.rst

@@ -1,6 +1,12 @@
 .. -*- rest -*-
 .. vim:syntax=rest
 
+|Coveralls|_
+
+.. |Coveralls| image:: https://coveralls.io/repos/nipy/nibabel/badge.png?branch=master
+.. _Coveralls: https://coveralls.io/r/nipy/nibabel?branch=master
+
+
 =======
 NiBabel
 =======

appveyor.yml

@@ -0,0 +1,45 @@
+# vim ft=yaml
+# CI on Windows via appveyor
+# This file was based on Olivier Grisel's python-appveyor-demo
+
+environment:
+
+  matrix:
+    - PYTHON: "C:\\Python27-conda32"
+      PYTHON_VERSION: "2.7"
+      PYTHON_ARCH: "32"
+
+    - PYTHON: "C:\\Python34-conda32"
+      PYTHON_VERSION: "3.4"
+      PYTHON_ARCH: "32"
+
+    - PYTHON: "C:\\Python34-conda64"
+      PYTHON_VERSION: "3.4"
+      PYTHON_ARCH: "64"
+
+install:
+  # Install miniconda Python
+  - "powershell ./tools/install_python.ps1"
+
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+
+  # Install the dependencies of the project.
+  - "conda install --yes --quiet numpy scipy matplotlib nose h5py"
+  - "pip install pydicom"
+  - "python setup.py install"
+  - "SET NIBABEL_DATA_DIR=%CD%\\nibabel-data"
+
+build: false  # Not a C# project, build stuff at the test step instead.
+
+test_script:
+  # Change into an innocuous directory and find tests from installation
+  - "mkdir for_testing"
+  - "cd for_testing"
+  - "nosetests --with-doctest nibabel"

bin/parrec2nii

@@ -103,6 +103,11 @@ def get_opt_parser():
                    store the corresponding settings in the NIfTI header, unless
                    non-uniform scaling is used, in which case the data is
                    stored in the file in scaled form. Default: 'dv'""")))
+    p.add_option(
+        Option('--keep-trace', action="store_true", dest='keep_trace',
+               default=False,
+               help=one_line("""Do not discard the diagnostic Philips DTI
+                             trace volume, if it exists in the data.""")))
     p.add_option(
         Option("--overwrite", action="store_true", dest="overwrite",
                default=False,
@@ -171,12 +176,26 @@ def proc_file(infile, opts):
     ornt = io_orientation(np.diag([-1, 1, 1, 1]).dot(affine))
     if np.all(ornt == [[0, 1],
                        [1, 1],
-                       [2, 1]]): # already in LAS+
+                       [2, 1]]):  # already in LAS+
         t_aff = np.eye(4)
-    else: # Not in LAS+
+    else:  # Not in LAS+
         t_aff = inv_ornt_aff(ornt, pr_img.shape)
         affine = np.dot(affine, t_aff)
         in_data = apply_orientation(in_data, ornt)
+
+    bvals, bvecs = pr_hdr.get_bvals_bvecs()
+    if not opts.keep_trace:  # discard Philips DTI trace if present
+        if bvals is not None:
+            bad_mask = np.logical_and(bvals != 0, (bvecs == 0).all(axis=1))
+            if bad_mask.sum() > 0:
+                pl = 's' if bad_mask.sum() != 1 else ''
+                verbose('Removing %s DTI trace volume%s'
+                        % (bad_mask.sum(), pl))
+                good_mask = ~bad_mask
+                in_data = in_data[..., good_mask]
+                bvals = bvals[good_mask]
+                bvecs = bvecs[good_mask]
+
     # Make corresponding NIfTI image
     nimg = nifti1.Nifti1Image(in_data, affine, pr_hdr)
     nhdr = nimg.header
@@ -208,7 +227,6 @@ def proc_file(infile, opts):
 
     # write out bvals/bvecs if requested
     if opts.bvs:
-        bvals, bvecs = pr_hdr.get_bvals_bvecs()
         if bvals is None and bvecs is None:
             verbose('No DTI volumes detected, bvals and bvecs not written')
         else:

nibabel/tests/test_scripts.py

@@ -52,6 +52,7 @@ def script_test(func):
 
 DATA_PATH = abspath(pjoin(dirname(__file__), 'data'))
 
+
 @script_test
 def test_nib_ls():
     # test nib-ls script
@@ -84,7 +85,7 @@ def test_nib_nifti_dx():
 
 
 def vox_size(affine):
-    return np.sqrt(np.sum(affine[:3,:3] ** 2, axis=0))
+    return np.sqrt(np.sum(affine[:3, :3] ** 2, axis=0))
 
 
 def check_conversion(cmd, pr_data, out_fname):
@@ -184,7 +185,7 @@ def test_parrec2nii_with_data():
             par_root, ext = splitext(basename(par))
             # NA.PAR appears to be a localizer, with three slices in each of
             # the three orientations: sagittal; coronal, transverse
-            if par_root ==  'NA':
+            if par_root == 'NA':
                 continue
             # Do conversion
             run_command(['parrec2nii', par])
@@ -226,8 +227,12 @@ def test_parrec2nii_with_data():
                                            check_code=False)
         assert_equal(code, 1)
         # Writes bvals, bvecs files if asked
-        run_command(['parrec2nii', '--overwrite', '--bvs', dti_par])
+        run_command(['parrec2nii', '--overwrite', '--keep-trace',
+                     '--bvs', dti_par])
         assert_almost_equal(np.loadtxt('DTI.bvals'), DTI_PAR_BVALS)
+        img = load('DTI.nii')
+        data = img.get_data().copy()
+        del img
         # Bvecs in header, transposed from PSL to LPS
         bvecs_LPS = DTI_PAR_BVECS[:, [2, 0, 1]]
         # Adjust for output flip of Y axis in data and bvecs
@@ -247,3 +252,19 @@ def test_parrec2nii_with_data():
         with open('DTI.dwell_time', 'rt') as fobj:
             contents = fobj.read().strip()
         assert_almost_equal(float(contents), exp_dwell)
+        # ensure trace is removed by default
+        run_command(['parrec2nii', '--overwrite', '--bvs', dti_par])
+        assert_true(exists('DTI.bvals'))
+        assert_true(exists('DTI.bvecs'))
+        img = load('DTI.nii')
+        bvecs_notrace = np.loadtxt('DTI.bvecs').T
+        bvals_notrace = np.loadtxt('DTI.bvals')
+        data_notrace = img.get_data().copy()
+        assert_equal(data_notrace.shape[-1], len(bvecs_notrace))
+        del img
+        # ensure correct volume was removed
+        good_mask = np.logical_or((bvecs_notrace != 0).any(axis=1),
+                                  bvals_notrace == 0)
+        assert_almost_equal(data_notrace, data[..., good_mask])
+        assert_almost_equal(bvals_notrace, np.array(DTI_PAR_BVALS)[good_mask])
+        assert_almost_equal(bvecs_notrace, bvecs_LAS[good_mask])

tools/install_python.ps1

@@ -0,0 +1,93 @@
+# Sample script to install Python and pip under Windows
+# Authors: Olivier Grisel, Jonathan Helmus and Kyle Kastner
+# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/
+
+$MINICONDA_URL = "http://repo.continuum.io/miniconda/"
+$BASE_URL = "https://www.python.org/ftp/python/"
+
+
+function DownloadMiniconda ($python_version, $platform_suffix) {
+    $webclient = New-Object System.Net.WebClient
+    if ($python_version -eq "3.4") {
+        $filename = "Miniconda3-3.5.5-Windows-" + $platform_suffix + ".exe"
+    } else {
+        $filename = "Miniconda-3.5.5-Windows-" + $platform_suffix + ".exe"
+    }
+    $url = $MINICONDA_URL + $filename
+
+    $basedir = $pwd.Path + "\"
+    $filepath = $basedir + $filename
+    if (Test-Path $filename) {
+        Write-Host "Reusing" $filepath
+        return $filepath
+    }
+
+    # Download and retry up to 3 times in case of network transient errors.
+    Write-Host "Downloading" $filename "from" $url
+    $retry_attempts = 2
+    for($i=0; $i -lt $retry_attempts; $i++){
+        try {
+            $webclient.DownloadFile($url, $filepath)
+            break
+        }
+        Catch [Exception]{
+            Start-Sleep 1
+        }
+   }
+   if (Test-Path $filepath) {
+       Write-Host "File saved at" $filepath
+   } else {
+       # Retry once to get the error message if any at the last try
+       $webclient.DownloadFile($url, $filepath)
+   }
+   return $filepath
+}
+
+
+function InstallMiniconda ($python_version, $architecture, $python_home) {
+    Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home
+    if (Test-Path $python_home) {
+        Write-Host $python_home "already exists, skipping."
+        return $false
+    }
+    if ($architecture -eq "32") {
+        $platform_suffix = "x86"
+    } else {
+        $platform_suffix = "x86_64"
+    }
+    $filepath = DownloadMiniconda $python_version $platform_suffix
+    Write-Host "Installing" $filepath "to" $python_home
+    $install_log = $python_home + ".log"
+    $args = "/S /D=$python_home"
+    Write-Host $filepath $args
+    Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru
+    if (Test-Path $python_home) {
+        Write-Host "Python $python_version ($architecture) installation complete"
+    } else {
+        Write-Host "Failed to install Python in $python_home"
+        Get-Content -Path $install_log
+        Exit 1
+    }
+}
+
+
+function InstallMinicondaPip ($python_home) {
+    $pip_path = $python_home + "\Scripts\pip.exe"
+    $conda_path = $python_home + "\Scripts\conda.exe"
+    if (-not(Test-Path $pip_path)) {
+        Write-Host "Installing pip..."
+        $args = "install --yes pip"
+        Write-Host $conda_path $args
+        Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru
+    } else {
+        Write-Host "pip already installed."
+    }
+}
+
+
+function main () {
+    InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON
+    InstallMinicondaPip $env:PYTHON
+}
+
+main