Merge branch 'read-the-docs' into 'dev'

Read the docs

See merge request !158

Author: wyli

niftynet/io/image_reader.py

@@ -81,6 +81,9 @@ def initialise(self, data_param, task_param, file_list):
         ``task_param`` specifies how to combine user input modalities.
         e.g., for multimodal segmentation 'image' corresponds to multiple
         modality sections, 'label' corresponds to one modality section
+
+        This function converts elements of ``file_list`` into
+        dictionaries of image objects, and save them to ``self.output_list``.
         """
         if not self.names:
             tf.logging.fatal('Please specify data input keywords, this should '
@@ -101,6 +104,7 @@ def initialise(self, data_param, task_param, file_list):
                                    for name in self.names)
         required_sections = \
             sum([list(vars(task_param).get(name)) for name in self.names], [])
+
         for required in required_sections:
             try:
                 if (file_list is None) or \
@@ -115,7 +119,14 @@ def initialise(self, data_param, task_param, file_list):
                     'file_list parameter should be a '
                     'pandas.DataFrame instance and has input '
                     'section name [%s] as a column name.', required)
+                if required_sections:
+                    tf.logging.fatal('Reader requires section(s): %s',
+                                     required_sections)
+                if file_list is not None:
+                    tf.logging.fatal('Configuration input sections are: %s',
+                                     list(file_list))
                 raise
+
         self._file_list = file_list
         self.output_list = _filename_to_image_list(
             self._file_list, self._input_sources, data_param)
@@ -284,16 +295,20 @@ def _filename_to_image_list(file_list, mod_dict, data_param):
     """
     volume_list = []
     for idx in range(len(file_list)):
+        # create image instance for each subject
         print_progress_bar(idx, len(file_list),
                            prefix='reading datasets headers',
                            decimals=1, length=10, fill='*')
+
         # combine fieldnames and volumes as a dictionary
         _dict = {}
         for field, modalities in mod_dict.items():
-            _dict[field] = _create_image(
-                file_list, idx, modalities, data_param)
+            _dict[field] = _create_image(file_list, idx, modalities, data_param)
+
+        # skipping the subject if there're missing image components
         if _dict and None not in list(_dict.values()):
             volume_list.append(_dict)
+
     if not volume_list:
         tf.logging.fatal(
             "Empty filename lists, please check the csv "

niftynet/io/image_sets_partitioner.py

@@ -61,7 +61,7 @@ class ImageSetsPartitioner(object):
     def initialise(self,
                    data_param,
                    new_partition=False,
-                   data_split_file="./test.csv",
+                   data_split_file=None,
                    ratios=None):
         """
         Set the data partitioner parameters
@@ -77,7 +77,10 @@ def initialise(self,
             and get_file_list always returns all subjects.
         """
         self.data_param = data_param
-        self.data_split_file = data_split_file
+        if data_split_file is None:
+            self.data_split_file = os.path.join('.', 'dataset_split.csv')
+        else:
+            self.data_split_file = data_split_file
         self.ratios = ratios
 
         self._file_list = None

niftynet/utilities/niftynet_global_config.py

@@ -73,7 +73,7 @@ def __load_or_create(config_file):
         creates a default one.
 
         :param config_file: no sanity checks are performed, as this
-        method is for internal use only
+            method is for internal use only
         :type config_file: `os.path`
         :returns: a dictionary of parsed configuration options
         :rtype: `dict`

niftynet/utilities/user_parameters_custom.py

@@ -19,7 +19,7 @@
 # Standardised string is defined in
 # niftynet.utilities.user_parameters_helper.standardise_string
 # the section name will be filtered with,
-# re.sub('[^0-9a-zA-Z ]+', '', input_string.strip())
+# re.sub('[^0-9a-zA-Z_\- ]+', '', input_string.strip())
 #
 # the value should be __add_mytask_args()
 #

niftynet/utilities/user_parameters_default.py

@@ -18,10 +18,10 @@
 
 
 def add_application_args(parser):
-    parser.add_argument(
-        "action",
-        help="train or inference",
-        choices=['train', 'inference'])
+    # parser.add_argument(
+    #     "action",
+    #     help="train or inference action",
+    #     choices=['train', 'inference'])
 
     parser.add_argument(
         "--cuda_devices",

niftynet/utilities/user_parameters_helper.py

@@ -53,7 +53,7 @@ def str_array(string_input):
     except ValueError:
         raise argparse.ArgumentTypeError(
             "list of strings expected, for each list element the allowed"
-            "characters: [ a-zA-Z0-9], but received {}".format(string_input))
+            "characters: [ a-zA-Z0-9_\-], but received {}".format(string_input))
     return output_tuple
 
 
@@ -98,7 +98,7 @@ def standardise_string(input_string):
     """
     if not isinstance(input_string, string_types):
         return input_string
-    new_name = re.sub('[^0-9a-zA-Z ]+', '', input_string.strip())
+    new_name = re.sub('[^0-9a-zA-Z_\- ]+', '', input_string.strip())
     return new_name
 
 

niftynet/utilities/user_parameters_parser.py

@@ -8,6 +8,7 @@
 
 import argparse
 import os
+import textwrap
 
 from niftynet.engine.application_factory import ApplicationFactory
 from niftynet.engine.application_factory import SUPPORTED_APP
@@ -42,25 +43,33 @@ def run():
     of the configuration file. based on the application_name
     or meta_parser.prog name, the section parsers are organised
     to find system parameters and application specific
-    parameters
+    parameters.
 
     :return: system parameters is a group of parameters including
         SYSTEM_SECTIONS and app_module.REQUIRED_CONFIG_SECTION
         input_data_args is a group of input data sources to be
         used by niftynet.io.ImageReader
     """
     meta_parser = argparse.ArgumentParser(
-        epilog=epilog_string)
+        description="Launch a NiftyNet application.",
+        formatter_class=argparse.RawDescriptionHelpFormatter,
+        epilog=textwrap.dedent(epilog_string))
     version_string = get_niftynet_version_string()
+    meta_parser.add_argument("action",
+                             help="train networks or run inferences",
+                             metavar='ACTION',
+                             choices=['train', 'inference'])
     meta_parser.add_argument("-v", "--version",
                              action='version',
                              version=version_string)
     meta_parser.add_argument("-c", "--conf",
-                             help="Specify configurations from a file",
-                             metavar="File", )
+                             help="specify configurations from a file",
+                             metavar="CONFIG_FILE")
     meta_parser.add_argument("-a", "--application_name",
-                             help="Specify application name",
-                             default="", )
+                             help="specify an application module name",
+                             metavar='APPLICATION_NAME',
+                             default="")
+
     meta_args, args_from_cmdline = meta_parser.parse_known_args()
     print(version_string)
 
@@ -70,13 +79,11 @@ def run():
               "forget '-c' command argument?{}".format(epilog_string))
         raise IOError
 
-    # Read global config file
-    global_config = NiftyNetGlobalConfig()
-
+    # Resolve relative configuration file location
     config_path = meta_args.conf
     if not os.path.isfile(config_path):
         relative_conf_file = os.path.join(
-            global_config.get_default_examples_folder(),
+            NiftyNetGlobalConfig().get_default_examples_folder(),
             config_path,
             config_path + "_config.ini")
         if os.path.isfile(relative_conf_file):
@@ -134,9 +141,11 @@ def run():
         '\nUnknown parameter: {}{}'.format(args_from_cmdline, epilog_string)
 
     # split parsed results in all_args
-    # into dictionary of system_args and input_data_args
+    # into dictionaries of system_args and input_data_args
     system_args = {}
     input_data_args = {}
+
+    # copy system default sections to ``system_args``
     for section in all_args:
         if section in SYSTEM_SECTIONS:
             system_args[section] = all_args[section]
@@ -148,6 +157,7 @@ def run():
         all_args['SYSTEM'].model_dir = os.path.join(
             os.path.dirname(meta_args.conf), 'model')
 
+    # copy non-default sections to ``input_data_args``
     for section in all_args:
         if section in SYSTEM_SECTIONS:
             continue
@@ -165,8 +175,9 @@ def run():
         else:
             input_data_args[section].csv_file = ''
 
-    # update conf path
+    # preserve ``config_file`` and ``action parameter`` from the meta_args
     system_args['CONFIG_FILE'] = argparse.Namespace(path=meta_args.conf)
+    system_args['SYSTEM'].action = meta_args.action
     return system_args, input_data_args
 
 
@@ -184,13 +195,14 @@ def _parse_arguments_by_section(parents,
 
     Commandline inputs only override system/custom parameters.
     input data related parameters needs to be defined in config file.
+
     :param parents: a list, parsers will be created as
-    subparsers of parents
+        subparsers of parents
     :param section: section name to be parsed
     :param args_from_config_file: loaded parameters from config file
     :param args_from_cmd: dictionary commandline parameters
     :return: parsed parameters of the section and unknown
-    commandline params.
+        commandline params.
     """
     section_parser = argparse.ArgumentParser(
         parents=parents,

tests/entry_point_test.py

@@ -54,15 +54,15 @@ def test_wrong_param(self):
             net_run.main()
 
     def test_empty(self):
-        with self.assertRaisesRegexp(IOError, ''):
+        with self.assertRaisesRegexp(SystemExit, ''):
             net_run.main()
-        with self.assertRaisesRegexp(IOError, ''):
+        with self.assertRaisesRegexp(SystemExit, ''):
             net_gan.main()
-        with self.assertRaisesRegexp(IOError, ''):
+        with self.assertRaisesRegexp(SystemExit, ''):
             net_segment.main()
-        with self.assertRaisesRegexp(IOError, ''):
+        with self.assertRaisesRegexp(SystemExit, ''):
             net_regress.main()
-        with self.assertRaisesRegexp(IOError, ''):
+        with self.assertRaisesRegexp(SystemExit, ''):
             net_autoencoder.main()