Merge branch 'image-loader' into 'dev'

Image loader

See merge request CMIC/NiftyNet!191

doc/source/config_spec.md

@@ -117,12 +117,13 @@ within each section.
 
 - [csv_file](#csv-file) :: `string` :: `csv_file=file_list.csv` :: `''`
 - [path_to_search](#path-to-search) :: `string` :: `path_to_search=my_data/fold_1` :: NiftyNet home folder
-- [filename_contain](#filename-contain) :: `String` or `string array` :: `filename_contain=foo, bar` :: `''`
+- [filename_contain](#filename-contain) :: `string` or `string array` :: `filename_contain=foo, bar` :: `''`
 - [filename_not_contain](#filename-not-contain) :: `string` or `string array` :: `filename_not_contain=foo` :: `''`
 - [interp_order](#interp-order) :: `integer` :: `interp_order=0` :: `3`
 - [pixdim](#pixdim) :: `float array` :: `pixdim=1.2, 1.2, 1.2` :: `''`
 - [axcodes](#axcodes) :: `string array` :: `axcodes=L, P, S` :: `''`
 - [spatial_window_size](#spatial-window-size) :: `integer array` :: `spatial_window_size=64, 64, 64` :: `''`
+- [loader](#loader) :: `string` :: `loader=simpleitk` :: `None`
 
 ###### `csv_file`
 A file path to a list of input images.  If the file exists, input image name
@@ -160,6 +161,11 @@ before fed into the network.
 Array of three integers specifies the input window size.
 Setting it to single slice, e.g., `spatial_window_size=64, 64, 1`, yields a 2-D slice window.
 
+###### `loader`
+Specify the loader to be used to load the files in the input section.
+Some loaders require additional Python packages.
+Default value `None` indicates trying all available loaders.
+
 This section will be used by [ImageReader](./niftynet.io.image_reader.html)
 to generate a list of [input images objects](./niftynet.io.image_type.html).
 For example:

niftynet/__init__.py

@@ -41,8 +41,8 @@
 from niftynet.io.misc_io import set_logger
 set_logger()
 
-from niftynet.utilities.util_import import check_module
-check_module('blinker', descriptor='New dependency', mandatory=True)
+from niftynet.utilities.util_import import require_module
+require_module('blinker', descriptor='New dependency', mandatory=True)
 
 import niftynet.utilities.util_common as util
 import niftynet.utilities.user_parameters_parser as user_parameters_parser

niftynet/contrib/evaluation/segmentation_evaluations.py

@@ -4,8 +4,9 @@
 
 import os
 
-from scipy import ndimage
+import numpy as np
 import pandas as pd
+from scipy import ndimage
 
 from niftynet.evaluation.base_evaluations import BaseEvaluation
 from niftynet.evaluation.segmentation_evaluations import \
@@ -18,15 +19,17 @@ class com_ref(PerComponentEvaluation):
     """
     Computes the centers of mass of each component in the reference standard
     """
+
     def metric_from_binarized(self, seg, ref):
         """
         :param seg: numpy array with binary mask from inferred segmentation
         :param ref: numpy array with binary mask from reference segmentation
         :return: dict of centers of mass in each axis
         """
-        return {d: 'com_ref_'+x
+        return {d: 'com_ref_' + x
                 for d, x in zip('XYZ', ndimage.center_of_mass(ref))}
 
+
 class ErrorMapsCC(BaseEvaluation):
     """
     Create 3 maps of connected component detection:
@@ -36,6 +39,7 @@ class ErrorMapsCC(BaseEvaluation):
     fpc_map shows all seg ccs that did not overlap any ref ccs
     Note we currently arbitrarily limit image generation to binary problems
     """
+
     def layer_op(self, subject_id, data):
         analyses = self.app_param.evaluation_units.split(',')
         if 'label' not in analyses and 'foreground' not in analyses:

niftynet/contrib/layer/rand_elastic_deform.py

@@ -6,15 +6,15 @@
 
 
 from __future__ import absolute_import, print_function
-from niftynet.utilities.util_import import check_module
-check_module('SimpleITK')
 
 import warnings
 
 import numpy as np
-import SimpleITK as sitk
 
 from niftynet.layer.base_layer import RandomisedLayer
+from niftynet.utilities.util_import import require_module
+
+sitk = require_module('SimpleITK')
 
 warnings.simplefilter("ignore", UserWarning)
 warnings.simplefilter("ignore", RuntimeWarning)

niftynet/contrib/segmentation_selective_sampler/test_sampler_selective.py

@@ -60,7 +60,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(7, 10, 2)
+        spatial_window_size=(7, 10, 2),
+        loader=None
     ),
     'FLAIR': ParserNamespace(
         csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
@@ -70,7 +71,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(7, 10, 2)
+        spatial_window_size=(7, 10, 2),
+        loader=None
     ),
     'Label': ParserNamespace(
         csv_file=os.path.join('testing_data', 'lesion.csv'),
@@ -80,7 +82,8 @@ def check_constraint(data, constraint):
         interp_order=1,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(7, 10, 2)
+        spatial_window_size=(7, 10, 2),
+        loader=None
     )
 }
 LABEL_TASK = {
@@ -92,7 +95,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(7, 10, 2)
+        spatial_window_size=(7, 10, 2),
+        loader=None
     )
 }
 MULTI_MOD_TASK = ParserNamespace(image=('T1', 'FLAIR'), label=('Label',))
@@ -106,7 +110,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(10, 9, 1)
+        spatial_window_size=(10, 9, 1),
+        loader=None
     ),
 }
 MOD_2D_TASK = ParserNamespace(image=('ultrasound',))
@@ -120,7 +125,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(8, 2)
+        spatial_window_size=(8, 2),
+        loader=None
     ),
     'FLAIR': ParserNamespace(
         csv_file=os.path.join('testing_data', 'FLAIRsampler.csv'),
@@ -130,7 +136,8 @@ def check_constraint(data, constraint):
         interp_order=3,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(8, 2)
+        spatial_window_size=(8, 2),
+        loader=None
     ),
     'Label': ParserNamespace(
         csv_file=os.path.join('testing_data', 'labels.csv'),
@@ -140,7 +147,8 @@ def check_constraint(data, constraint):
         interp_order=1,
         pixdim=None,
         axcodes=None,
-        spatial_window_size=(8, 2)
+        spatial_window_size=(8, 2),
+        loader=None
     )
 }