Moved the QC assets into the spinalcordtoolbox package

MANIFEST.in

@@ -1,13 +1,11 @@
 include LICENSE
 include setup*
 include README*
-include Changelog
+include CHANGES.md
 include abstract.png
 include version.txt
-include batch_processing*
 
-recursive-include testing *.py *.sh
-recursive-exclude testing __MACOSX
-
-recursive-include scripts *.py
-recursive-exclude scripts __MACOSX
+graft spinalcordtoolbox/reports/assets
+prune dev
+prune scripts
+prune testing

install_sct

@@ -426,7 +426,7 @@ fi
 
 
 ## Install the spinalcordtoolbox into conda
-pip install -e ${SCT_SOURCE}
+pip install ${SCT_SOURCE}
 
 
 ## Install binaries

scripts/sct_label_vertebrae.py

@@ -18,10 +18,8 @@
 # TODO: address the case when there is more than one max correlation
 
 import sys
-# import commands
 import os
 import shutil
-# from glob import glob
 import numpy as np
 from sct_maths import mutual_information
 from msct_parser import Parser
@@ -351,7 +349,7 @@ def test(qslice):
  return qslice.single()
 
  labeled_seg_file = path_output + file_seg + '_labeled' + ext_seg
- test(qcslice.Sagittal(fname_in, labeled_seg_file))
+ test(qcslice.Sagittal(Image(fname_in), Image(labeled_seg_file)))
  sct.printv('Sucessfully generated the QC results in %s' % qc_param.qc_results)
  sct.printv('Use the following command to see the results in a browser:')
  sct.printv('sct_qc -folder %s' % qc_path, type='info')

scripts/sct_propseg.py

@@ -596,11 +596,10 @@ def get_parser():
  def test(qslice):
  return qslice.mosaic()
 
- test(qcslice.Axial(fname_input_data, fname_seg))
+ test(qcslice.Axial(Image(fname_input_data), Image(fname_seg)))
  sct.printv('Sucessfully generated the QC results in %s' % param.qc_results)
  sct.printv('Use the following command to see the results in a browser:')
  sct.printv('sct_qc -folder %s' % qc_path, type='info')
 
  sct.printv('\nDone! To view results, type:', verbose)
  sct.printv("fslview " + fname_input_data + " " + fname_seg + " -l Red -b 0,1 -t 0.7 &\n", verbose, 'info')
-

scripts/sct_qc.py

@@ -5,6 +5,9 @@
 # Copyright (c) 2017 Polytechnique Montreal <www.neuro.polymtl.ca>
 # About the license: see the file LICENSE.TXT
 
+"""Simple local http server to serve QC reports
+"""
+
 import os
 import shutil
 import sys
@@ -14,6 +17,8 @@
 from msct_parser import Parser
 from sct_utils import printv
 
+import spinalcordtoolbox.reports as reports
+
 
 def get_parser():
  parser = Parser(__file__)
@@ -27,8 +32,7 @@ def get_parser():
 
 
 def _copy_assets(dest_path):
- home_dir = os.path.dirname(os.path.dirname(__file__))
- assets_path = os.path.join(home_dir, 'assets')
+ assets_path = os.path.join(reports.__path__[0], 'assets')
 
  shutil.copy2(os.path.join(assets_path, 'index.html'), dest_path)
 
@@ -63,4 +67,7 @@ def _copy_assets(dest_path):
  printv('http://127.0.0.1:8888', type='info')
  printv('Copy and paste the address into your web browser')
  printv('Press "Ctrl" + "C" to stop sct_qc')
- httpd.serve_forever()
+ try:
+ httpd.serve_forever()
+ except KeyboardInterrupt:
+ printv('QC viewer stopped')

scripts/sct_register_to_template.py

@@ -567,12 +567,12 @@ def main():
  qc_param = qc.Params(fname_data, 'sct_register_to_template', args, 'Sagittal', qc_path)
  report = qc.QcReport(qc_param, '')
 
- @qc.QcImage(report, 'bicubic', [qc.QcImage.no_seg_seg])
+ @qc.QcImage(report, 'none', [qc.QcImage.no_seg_seg])
  def test(qslice):
  return qslice.single()
 
  fname_template2anat = path_output + 'template2anat' + ext_data
- test(qcslice.SagittalTemplate2Anat(fname_data, fname_template2anat, fname_seg))
+ test(qcslice.SagittalTemplate2Anat(Image(fname_data), Image(fname_template2anat), Image(fname_seg)))
  sct.printv('Sucessfully generate the QC results in %s' % qc_param.qc_results)
  sct.printv('Use the following command to see the results in a browser')
  sct.printv('sct_qc -folder %s' % qc_path, type='info')

setup.cfg

@@ -13,7 +13,7 @@ source = spinalcordtoolbox/
 
 [flake8]
 exclude = build,.git,.tox,
-ignore = E501
+ignore = E501,E402
 max-line-length = 179
 
 [isort]

setup.py

@@ -13,10 +13,11 @@
  requirements = f.read().splitlines()
 
 with open(path.join(here, 'version.txt')) as f:
- version = f.read().split()
+ version = f.read().strip()
 
 setup(
  name='spinalcordtoolbox',
+ version=version,
  description='Library of analysis tools for MRI of the spinal cord',
  long_description=long_description,
  url='http://www.neuro.polymtl.ca/home',
@@ -37,12 +38,13 @@
  'Programming Language :: Python :: 2.7',
  ],
  keywords='Magnetic Resonance Imaging MRI spinal cord analysis template',
- packages=find_packages(exclude=['dev', 'install']),
+ packages=find_packages(exclude=['scripts', 'dev', 'dev.*', 'install', 'testing']),
+ package_data={},
  install_requires=requirements,
  include_package_data=True,
 
  # To provide executable scripts, use entry points in preference to the
  # "scripts" keyword. Entry points provide cross-platform support and allow
  # pip to create the appropriate form of executable for the target platform.
- entry_points={'console_scripts': ['sct=spinalcordtoolbox.qc.serve:spinalcordtoolbox'], },
+ # entry_points={'console_scripts': ['sct=spinalcordtoolbox.qc.serve:spinalcordtoolbox'], },
 )

spinalcordtoolbox/reports/qc.py

@@ -5,10 +5,8 @@
 import subprocess
 
 import warnings
-
-import shutil
-
 warnings.filterwarnings("ignore")
+
 import datetime
 import matplotlib
 matplotlib.use('Agg')
@@ -202,7 +200,7 @@ def _save(self, img_path, format='png', bbox_inches='tight', pad_inches=0.00):
 class Params(object):
  """Parses and stores the variables that will included into the QC details
 
- We derive the value of the contrast and subject name from the `input_file` path, 
+ We derive the value of the contrast and subject name from the `input_file` path,
  by splitting it into `[subject]/[contrast]/input_file`
  """
 
@@ -211,7 +209,7 @@ def __init__(self, input_file, command, args, orientation, dest_folder):
  Parameters
  ----------
  input_file : str
- the input nifti file name 
+ the input nifti file name
  command : str
  the command name
  args : str
@@ -294,28 +292,19 @@ def update_description_file(self, dimension):
 
  Parameters
  ----------
- unparsed_args : list of str
- the commands used in the Terminal of the process
  description : str
  quick description of current usage of the process
- sct_commit : str
- commit version of the code being currently used to generate the images
  """
  # get path of the toolbox
- path_script = os.path.dirname(__file__)
- path_sct = os.path.dirname(path_script)
- with open(os.path.join(path_sct, '..', 'version.txt')) as file_handle:
- sct_version = file_handle.read().strip()
-
  try:
- cmd = 'git log -n 1 --pretty=format:"%H"'.split()
+ cmd = 'git rev-parse --short HEAD'.split()
  git_hash = subprocess.check_output(cmd).strip('"')
  except subprocess.CalledProcessError:
  git_hash = "N/A"
 
  output = {
  'command': self.qc_params.command,
- 'version': "{}({})".format(sct_version, git_hash),
+ 'version': git_hash,
  'args': ' '.join(self.qc_params.args),
  'subject': self.qc_params.subject,
  'contrast': self.qc_params.contrast,

spinalcordtoolbox/reports/slice.py

@@ -8,7 +8,6 @@
 import numpy as np
 from scipy import ndimage
 
-import scripts.msct_image as msct_image
 
 logger = logging.getLogger(__name__)
 
@@ -34,13 +33,13 @@ def __init__(self, image_name, seg_image_name):
  """
  Parameters
  ----------
- image_name : str
+ image_name : msct_image.Image
  Input 3D MRI to be separated into slices.
- seg_image_name : str
+ seg_image_name : msct_image.Image
  Output name for the 3D MRI to be produced.
  """
- self.image = msct_image.Image(image_name)
- self.image_seg = msct_image.Image(seg_image_name)
+ self.image = image_name
+ self.image_seg = seg_image_name
  self.image.change_orientation('SAL')
  self.image_seg.change_orientation('SAL')
 
@@ -118,7 +117,7 @@ def crop(matrix, x, y, width, height):
  returns the cropped matrix
  """
  if width * 2 > matrix.shape[0]:
- width = matrix.shape[0] // 2
+  width = matrix.shape[0] // 2
  if height * 2 > matrix.shape[1]:
  height = matrix.shape[1] // 2
 
@@ -347,7 +346,7 @@ class AxialTemplate2Anat(AxialTemplate):
  """The axial template to anat representation of a slice"""
  def __init__(self, image_name, template2anat_image_name, seg_image_name):
  super(AxialTemplate2Anat, self).__init__(image_name, template2anat_image_name)
- self.image_seg2 = msct_image.Image(seg_image_name) # transformed input the one segmented
+ self.image_seg2 = seg_image_name # transformed input the one segmented
  self.image_seg2.change_orientation('SAL') # reorient to SAL
 
  def get_center(self):
@@ -410,7 +409,7 @@ class SagittalTemplate2Anat(Sagittal):
 
  def __init__(self, image_name, template2anat_name, seg_image_name):
  super(SagittalTemplate2Anat, self).__init__(image_name, template2anat_name)
- self.image_seg2 = msct_image.Image(seg_image_name) # transformed input the one segmented
+ self.image_seg2 = seg_image_name # transformed input the one segmented
  self.image_seg2.change_orientation('SAL') # reorient to SAL
 
  def get_center(self):