Moved client code back into repo; items in imagej directory won't run in server environment

clients/examples/run_simple_ilastik.py

+from clients.util import get_client
+from clients import ilastik_map_objects_simple
+
+if __name__ == '__main__':
+
+    img_abspath = 'C:\\Users\\rhodes\\projects\\proj0004-marine-photoactivation\\data\\exp0021\\B2\\20230320-153317\\Selection\\Selection--W0000--P0001-T0001.czi'
+
+    params = {
+        'pixel_classifier_path': 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0019/px-02.ilp',
+        'object_classifier_path': 'c:/Users/rhodes/projects/proj0011-plankton-seg/exp0019/obj-06.ilp',
+        'channel': 4,
+    }
+
+    outfile = ilastik_map_objects_simple.main(
+        get_client(port=6221),
+        img_abspath,
+        params
+    )
+    print(f'Success: {outfile}')
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clients/ilastik_map_objects_simple.py

+from os.path import basename, dirname
+
+def main(request_func, in_abspath, params):
+
+	where = dirname(in_abspath)
+	in_file = basename(in_abspath)
+	
+	px_ilp = params['pixel_classifier_path']
+	ob_ilp = params['object_classifier_path']
+	channel = params['channel']
+	
+	# configure input and output paths
+	resp = request_func(
+		'PUT',
+		'/paths/watch_input',
+		{
+			'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,
+		},
+	)
+	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,
+		}
+	)
+	assert resp['status'] == 200, 'Error calling workfow'
+	return resp['content']['object_map_filepath']
+	

clients/imagej/adapter.py

+import httplib
+import json
+import urllib
+
+from ij import ImagePlus
+
+HOST = '127.0.0.1'
+PORT = 6221
+uri = 'http://{}:{}/'.format(HOST, PORT)
+
+def hit_endpoint(method, endpoint, params=None):
+    connection = httplib.HTTPConnection(HOST, PORT)
+    if not method in ['GET', 'PUT']:
+        raise Exception('Can only handle GET and PUT requests')
+    if params:
+        url = endpoint + '?' + urllib.urlencode(params)
+    else:
+        url = endpoint
+    connection.request(method, url)
+    resp = connection.getresponse()
+    resp_str = resp.read()
+    try:
+    	content = json.loads(resp_str)
+    except Exception:
+    	content = {'str': str(resp_str)}
+    return {'status': resp.status, 'content': content
+}
+
+def run_request_sequence(imp, module, params):
+	in_path = imp.getProp('Location')
+	out_path = func(hit_endpoint, in_path, params)
+	return ImagePlus(out_path)
\ No newline at end of file

clients/util.py

+import requests
+
+def get_client(host='127.0.0.1', port=8000):
+    """Return a client wrapper for testing in same python 3.9 environment as server"""
+    uri = f'http://{host}:{port}'
+
+    def hit_endpoint(method, endpoint, params=None):
+        if method == 'GET':
+            resp = requests.get(uri + endpoint)
+        elif method == 'PUT':
+            resp = requests.put(uri + endpoint, params=params)
+        else:
+            raise Exception('Can only handle GET and PUT requests')
+        if resp.status_code != 200:
+            return {'status': resp.status_code, 'content': resp.text}
+        else:
+            return {'status': resp.status_code, 'content': resp.json()}
+    return hit_endpoint
\ No newline at end of file