From 30f37e0b335c34d181592863678a9eb29154c77b Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Fri, 3 Nov 2023 15:26:02 +0100
Subject: [PATCH] Moved client code back into repo; items in imagej directory
won't run in server environment
---
clients/__init__.py | 0
clients/examples/__init__.py | 0
clients/examples/run_simple_ilastik.py | 19 ++++++++
clients/ilastik_map_objects_simple.py | 67 ++++++++++++++++++++++++++
clients/imagej/__init__.py | 0
clients/imagej/adapter.py | 32 ++++++++++++
clients/util.py | 18 +++++++
7 files changed, 136 insertions(+)
create mode 100644 clients/__init__.py
create mode 100644 clients/examples/__init__.py
create mode 100644 clients/examples/run_simple_ilastik.py
create mode 100644 clients/ilastik_map_objects_simple.py
create mode 100644 clients/imagej/__init__.py
create mode 100644 clients/imagej/adapter.py
create mode 100644 clients/util.py
diff --git a/clients/__init__.py b/clients/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/clients/examples/__init__.py b/clients/examples/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/clients/examples/run_simple_ilastik.py b/clients/examples/run_simple_ilastik.py
new file mode 100644
index 00000000..de420baa
--- /dev/null
+++ b/clients/examples/run_simple_ilastik.py
@@ -0,0 +1,19 @@
+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}')
\ No newline at end of file
diff --git a/clients/ilastik_map_objects_simple.py b/clients/ilastik_map_objects_simple.py
new file mode 100644
index 00000000..3fae8a87
--- /dev/null
+++ b/clients/ilastik_map_objects_simple.py
@@ -0,0 +1,67 @@
+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']
+
diff --git a/clients/imagej/__init__.py b/clients/imagej/__init__.py
new file mode 100644
index 00000000..e69de29b
diff --git a/clients/imagej/adapter.py b/clients/imagej/adapter.py
new file mode 100644
index 00000000..1bdd36de
--- /dev/null
+++ b/clients/imagej/adapter.py
@@ -0,0 +1,32 @@
+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
diff --git a/clients/util.py b/clients/util.py
new file mode 100644
index 00000000..2038bbcf
--- /dev/null
+++ b/clients/util.py
@@ -0,0 +1,18 @@
+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
--
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