Example script with 3D ilastik model

examples/ilastik3d.py

+from multiprocessing import Process
+from pathlib import Path
+import requests
+from shutil import copyfile
+
+import uvicorn
+
+host = '127.0.0.1'
+port = 5001
+px3d_ilp = '3d_model/px3d.ilp'
+ob3d_ilp = '3d_model/ob3d.ilp'
+
+czi_root = Path('z:/rhodes/projects/proj0004-marine-photoactivation/data/exp0036')
+czis = [
+    'A01-selection-test01.czi',
+    'B01-selection-test01.czi'
+]
+channel = 4
+
+if __name__ == '__main__':
+    server_process = Process(
+        target=uvicorn.run,
+        args=('api:app',),
+        kwargs={'host': host, 'port': port, 'log_level': 'debug'},
+        daemon=True
+    )
+    uri = f'http://{host}:{port}/'
+    server_process.start()
+
+    resp_paths = requests.get(uri + 'paths')
+    paths = resp_paths.json()
+
+    # load ilastik pixel model
+    resp_load_px = requests.put(
+        uri + 'models/ilastik/pixel_classification/load/',
+        params={'project_file': px3d_ilp},
+    )
+    assert resp_load_px.status_code == 200
+    model_id_px = resp_load_px.json()['model_id']
+
+    # load ilastik object model
+    resp_load_ob = requests.put(
+        uri + 'models/ilastik/object_classification/load/',
+        params={'project_file': ob3d_ilp},
+    )
+    assert resp_load_ob.status_code == 200
+    model_id_ob = resp_load_ob.json()['model_id']
+
+    # copy files from network storage to processing directory
+    for ff in czis:
+        infile = Path(czi_root) / ff
+        outfile = Path(paths['inbound_images']) / ff
+        copyfile(infile, outfile)
+
+        # infer pixel maps
+        resp_infer_px = requests.put(
+            uri + f'infer/from_image_file',
+            params={
+                'model_id': model_id_px,
+                'input_filename': ff,
+                'channel': channel,
+            },
+        )
+        assert resp_infer_px == 200
+
+        # infer object maps
+        resp_infer_ob = requests.put(
+            uri + f'infer/from_image_file',
+            params={
+                'model_id': model_id_ob,
+                'input_filename': ff,
+                'channel': channel,
+            },
+        )
+        assert resp_infer_px == 200
+
+    resp_models = requests.get(uri + 'models')
+
+    server_process.terminate()
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