Initial Python API changes for cmake adoption

python/bin/mrtrix3.py

@@ -14,53 +14,19 @@
 #
 # For more details, see http://www.mrtrix.org/.
 
-import imp, os, sys
-
-def imported(lib_path):
-  success = False
-  fp = None
-  try:
-    fp, pathname, description = imp.find_module('mrtrix3', [ lib_path ])
-    imp.load_module('mrtrix3', fp, pathname, description)
-    success = True
-  except ImportError:
-    pass
-  finally:
-    if fp:
-      fp.close()
-  return success
-
-# Can the MRtrix3 Python modules be found based on their relative location to this file?
-# Note that this includes the case where this file is a softlink within an external module,
-# which provides a direct link to the core installation
-if not imported (os.path.normpath (os.path.join ( \
-  os.path.dirname (os.path.realpath (__file__)), os.pardir, 'lib') )):
-
-  # If this file is a duplicate, which has been stored in an external module,
-  # we may be able to figure out the location of the core library using the
-  # build script.
-
-  # case 1: build is a symbolic link:
-  if not imported (os.path.join (os.path.dirname (os.path.realpath ( \
-      os.path.join (os.path.dirname(__file__), os.pardir, 'build'))), 'lib')):
-
-    # case 2: build is a file containing the path to the core build script:
-    try:
-      with open (os.path.join (os.path.dirname(__file__), os.pardir, 'build')) as fp:
-        for line in fp:
-          build_path = line.split ('#',1)[0].strip()
-          if build_path:
-            break
-    except IOError:
-      pass
-
-    if not imported (os.path.join (os.path.dirname (build_path), 'lib')):
-
-      sys.stderr.write('''
+import importlib, os, sys
+
+try:
+  spec = importlib.util.spec_from_file_location('mrtrix3', os.path.normpath(os.path.join(os.path.realpath(__file__), '..', 'lib', 'mrtrix3', '__init__.py')))
+  module = importlib.util.module_from_spec(spec)
+  sys.modules[spec.name] = module
+  spec.loader.exec_module(module)
+except ImportError:
+  sys.stderr.write('''
 ERROR: Unable to locate MRtrix3 Python modules
 
 For detailed instructions, please refer to:
 https://mrtrix.readthedocs.io/en/latest/tips_and_tricks/external_modules.html
 ''')
-      sys.stderr.flush()
-      sys.exit(1)
+  sys.stderr.flush()
+  sys.exit(1)

python/lib/mrtrix3/__init__.py

@@ -39,7 +39,9 @@ class MRtrixError(MRtrixBaseError): #pylint: disable=unused-variable
 # Location of binaries that belong to the same MRtrix3 installation as the Python library being invoked
 BIN_PATH = os.path.abspath(os.path.join(os.path.abspath(os.path.dirname(os.path.abspath(__file__))), os.pardir, os.pardir, 'bin'))
 # Must remove the '.exe' from Windows binary executables
-EXE_LIST = [ os.path.splitext(name)[0] for name in os.listdir(BIN_PATH) ] #pylint: disable=unused-variable
+# TODO This needs to be read from a new file to be written by cmake --build;
+#   can't assume that binaries directory is not populated with other contents
+EXE_LIST = [ ] #pylint: disable=unused-variable
 
 
 # 'CONFIG' is a dictionary containing those entries present in the MRtrix config files

python/lib/mrtrix3/algorithm.py

@@ -23,10 +23,15 @@
 
 
 # Helper function for finding where the files representing different script algorithms will be stored
-# These will be in a sub-directory relative to this library file
+# These will be in a sub-directory relative to the executed file
 def _algorithms_path():
   from mrtrix3 import path #pylint: disable=import-outside-toplevel
-  return os.path.realpath(os.path.join(os.path.dirname(os.path.realpath(inspect.getouterframes(inspect.currentframe())[-1][1])), os.pardir, 'lib', 'mrtrix3', path.script_subdir_name()))
+  sys.stderr.write(os.path.realpath(inspect.getouterframes(inspect.currentframe())[-1][1]) + '\n')
+  return os.path.realpath(os.path.join(os.path.dirname(os.path.realpath(inspect.getouterframes(inspect.currentframe())[-1][1])),
+                                       os.pardir,
+                                       'src',
+                                       'mrtrix3',
+                                       path.script_srcdir_name()))
 
 
 
@@ -54,10 +59,13 @@ def usage(cmdline): #pylint: disable=unused-variable
   # Don't let Python 3 try to read incompatible .pyc files generated by Python 2 for no-longer-existent .py files
   pylist = get_list()
   base_parser = app.Parser(description='Base parser for construction of subparsers', parents=[cmdline])
-  subparsers = cmdline.add_subparsers(title='Algorithm choices', help='Select the algorithm to be used to complete the script operation; additional details and options become available once an algorithm is nominated. Options are: ' + ', '.join(get_list()), dest='algorithm')
+  subparsers = cmdline.add_subparsers(title='Algorithm choices',
+                                      help='Select the algorithm to be used to complete the script operation; '
+                                           'additional details and options become available once an algorithm is nominated. '
+                                           'Options are: ' + ', '.join(get_list()), dest='algorithm')
   for dummy_importer, package_name, dummy_ispkg in pkgutil.iter_modules( [ _algorithms_path() ] ):
     if package_name in pylist:
-      module = importlib.import_module(path.script_subdir_name() + '.' + package_name)
+      module = importlib.import_module(path.script_srcdir_name() + '.' + package_name)
       module.usage(base_parser, subparsers)
       initlist.extend(package_name)
   app.debug('Initialised algorithms: ' + str(initlist))
@@ -66,4 +74,4 @@ def usage(cmdline): #pylint: disable=unused-variable
 
 def get_module(name): #pylint: disable=unused-variable
   from mrtrix3 import path #pylint: disable=import-outside-toplevel
-  return sys.modules[path.script_subdir_name() + '.' + name]
+  return sys.modules[path.script_srcdir_name() + '.' + name]

python/lib/mrtrix3/path.py

@@ -17,7 +17,7 @@
 
 
 
-import ctypes, errno, inspect, os, random, shlex, shutil, string, subprocess, time
+import ctypes, errno, inspect, os, random, shlex, shutil, string, subprocess, sys, time
 from mrtrix3 import CONFIG
 
 
@@ -117,10 +117,10 @@ def name_temporary(suffix): #pylint: disable=unused-variable
 
 
 # Determine the name of a sub-directory containing additional data / source files for a script
-# This can be algorithm files in lib/mrtrix3/, or data files in share/mrtrix3/
+# This can be algorithm files in src/mrtrix3/, or data files in share/mrtrix3/
 # This function appears here rather than in the algorithm module as some scripts may
 #   need to access the shared data directory but not actually be using the algorithm module
-def script_subdir_name(): #pylint: disable=unused-variable
+def script_srcdir_name(): #pylint: disable=unused-variable
   from mrtrix3 import app #pylint: disable=import-outside-toplevel
   frameinfo = inspect.stack()[-1]
   try:

python/lib/mrtrix3/run.py

@@ -550,7 +550,7 @@ def exe_name(item):
 def version_match(item):
   from mrtrix3 import app #pylint: disable=import-outside-toplevel
   if not item in EXE_LIST:
-    app.debug('Command ' + item + ' not found in MRtrix3 bin/ directory')
+    app.debug('Command ' + item + ' not an MRtrix3 executable')
     return item
   exe_path_manual = os.path.join(BIN_PATH, exe_name(item))
   if os.path.isfile(exe_path_manual):

python/lib/mrtrix3/_5ttgen/freesurfer.py → python/src/mrtrix3/_5ttgen/freesurfer.py

@@ -56,7 +56,7 @@ def execute(): #pylint: disable=unused-variable
     lut_output_file_name = 'FreeSurfer2ACT_sgm_amyg_hipp.txt'
   else:
     lut_output_file_name = 'FreeSurfer2ACT.txt'
-  lut_output_path = os.path.join(path.shared_data_path(), path.script_subdir_name(), lut_output_file_name)
+  lut_output_path = os.path.join(path.shared_data_path(), path.script_srcdir_name(), lut_output_file_name)
   if not os.path.isfile(lut_output_path):
     raise MRtrixError('Could not find lookup table file for converting FreeSurfer parcellation output to tissues (expected location: ' + lut_output_path + ')')
 

python/lib/mrtrix3/_5ttgen/hsvs.py → python/src/mrtrix3/_5ttgen/hsvs.py

@@ -288,10 +288,10 @@ def execute(): #pylint: disable=unused-variable
       raise MRtrixError('FREESURFER_HOME environment variable not set; required for use of hippocampal subfields module')
     freesurfer_lut_file = os.path.join(os.environ['FREESURFER_HOME'], 'FreeSurferColorLUT.txt')
     check_file(freesurfer_lut_file)
-    hipp_lut_file = os.path.join(path.shared_data_path(), path.script_subdir_name(), 'hsvs', 'HippSubfields.txt')
+    hipp_lut_file = os.path.join(path.shared_data_path(), path.script_srcdir_name(), 'hsvs', 'HippSubfields.txt')
     check_file(hipp_lut_file)
     if hipp_subfield_has_amyg:
-      amyg_lut_file = os.path.join(path.shared_data_path(), path.script_subdir_name(), 'hsvs', 'AmygSubfields.txt')
+      amyg_lut_file = os.path.join(path.shared_data_path(), path.script_srcdir_name(), 'hsvs', 'AmygSubfields.txt')
       check_file(amyg_lut_file)
 
   if app.ARGS.sgm_amyg_hipp: