Added docstrings

clients/examples/run_simple_ilastik.py

+"""
+Debug a client request sequence from the same environment as the server
+"""
+
 from clients.util import get_client
 from clients import ilastik_map_objects_simple
 

clients/ilastik_map_objects_simple.py

-from os.path import basename, dirname
+from os.path import basename, dirname
+
 
 def main(request_func, in_abspath, params):
+	"""
+	Execute a sequence of client requests that load ilastik pixel and object classifiers, then infer on an image file
+	:param request_func: (func) function that implements HTTP client, dependent on which environment request are called from
+	:param in_abspath: (str) absolute path to image file to infer
+	:param params:
+		pixel_classifier_path: (str) absolute path to ilastik project file that defines a pixel classifier
+		object_classifier_path: (str) absolute path to ilastik project file that defines an object classifier
+		channel: (int) channel of the input image to process
+	:return: (str) absolute path where a new object map is written
+	"""
 
 	where = dirname(in_abspath)
 	in_file = basename(in_abspath)
@@ -9,59 +20,59 @@ def main(request_func, in_abspath, params):
 	ob_ilp = params['object_classifier_path']
 	channel = params['channel']
 	
-	# configure input and output paths
-	resp = request_func(
-		'PUT',
+	# configure input and output paths
+	resp = request_func(
+		'PUT',
 		'/paths/watch_input',
-		{
-			'path': where,
-		}
-	)
-	assert resp['status'] == 200, 'Error setting up image directory'
+		{
+			'path': where,
+		}
+	)
+	assert resp['status'] == 200, 'Error setting up image directory'
 	
-	resp = request_func(
-		'PUT',
-		'/paths/watch_output',
-		{
-			'path': where,
-		}
-	)
-	assert resp['status'] == 200, 'Error setting up image directory'
-	
-	# load pixel classifier
-	resp = request_func(
-		'PUT',
-		'/ilastik/px/load/',
-		{
-			'project_file': px_ilp,
-			'duplicate': False,
-		},
-	)
+	resp = request_func(
+		'PUT',
+		'/paths/watch_output',
+		{
+			'path': where,
+		}
+	)
+	assert resp['status'] == 200, 'Error setting up image directory'
+	
+	# load pixel classifier
+	resp = request_func(
+		'PUT',
+		'/ilastik/px/load/',
+		{
+			'project_file': px_ilp,
+			'duplicate': False,
+		},
+	)
 	assert resp['status'], 'Error loading classifier: ' + px_ilp
 	id_px_mod = resp['content']['model_id']
-	
-	# load object classifier
-	resp = request_func(
-		'PUT', '/ilastik/pxmap_to_obj/load/',
-		{
-			'project_file': ob_ilp,
-			'duplicate': False,
-		},
-	)
-	assert resp['status'] == 200, 'Error loading object classifier: ' + {ob_ilp}
-	id_ob_mod = resp['content']['model_id']
-	
-	# run inference
-	resp = request_func(
-		'PUT',
-		'/ilastik/pixel_then_object_classification/infer',
-		{
-			'px_model_id': id_px_mod,
-			'ob_model_id': id_ob_mod,
-			'input_filename': in_file,
-			'channel': channel,
-		}
+	
+	# load object classifier
+	resp = request_func(
+		'PUT', '/ilastik/pxmap_to_obj/load/',
+		{
+			'project_file': ob_ilp,
+			'duplicate': False,
+		},
+	)
+	assert resp['status'] == 200, 'Error loading object classifier: ' + {ob_ilp}
+	id_ob_mod = resp['content']['model_id']
+	
+	# run inference
+	resp = request_func(
+		'PUT',
+		'/ilastik/pixel_then_object_classification/infer',
+		{
+			'px_model_id': id_px_mod,
+			'ob_model_id': id_ob_mod,
+			'input_filename': in_file,
+			'channel': channel,
+		}
 	)
 	assert resp['status'] == 200, 'Error calling workfow'
-	return resp['content']['object_map_filepath']
-	
+	return resp['content']['object_map_filepath']
+	

clients/imagej/adapter.py

+"""
+Functionality needed to run a client request sequence (clients.*.main) in the ImageJ python 2.7 script environment
+"""
+
 import httplib
 import json
 import urllib
@@ -9,6 +13,13 @@ PORT = 6221
 uri = 'http://{}:{}/'.format(HOST, PORT)
 
 def hit_endpoint(method, endpoint, params=None):
+    """
+    Python 2.7 implementation of HTTP client
+    :param method: (str) either 'GET' or 'PUT'
+    :param endpoint: (str) endpoint of HTTP request
+    :param params: (dict) of parameters required by client request
+    :return: (dict) of response status and content, formatted as dict if request is successful
+    """
     connection = httplib.HTTPConnection(HOST, PORT)
     if not method in ['GET', 'PUT']:
         raise Exception('Can only handle GET and PUT requests')
@@ -23,10 +34,16 @@ def hit_endpoint(method, endpoint, params=None):
     	content = json.loads(resp_str)
     except Exception:
     	content = {'str': str(resp_str)}
-    return {'status': resp.status, 'content': content
-}
+    return {'status': resp.status, 'content': content}
 
-def run_request_sequence(imp, module, params):
+def run_request_sequence(imp, func, params):
+    """
+    Execute a sequence of client requests in the ImageJ scripting environment
+    :param imp: (ij.ImagePlus) input image
+    :param func: (func) function that implements client request sequence
+    :param params: (dict) parameters specific to client request
+    :return: (ij.ImagePlus) output image
+    """
 	in_path = imp.getProp('Location')
 	out_path = func(hit_endpoint, in_path, params)
 	return ImagePlus(out_path)
\ No newline at end of file