Unfinished changes to automic simulator and testing 3D ilastik model

api.py

-from typing import Dict
-
 from fastapi import FastAPI, HTTPException
 
 from model_server.ilastik import IlastikPixelClassifierModel, IlastikObjectClassifierModel

imagej/infer_ilastik_by_api.py

@@ -17,7 +17,7 @@ input_filename = os.path.split(abspath)[-1]
 
 outpath = 'C:\\Users\\rhodes\\projects\\proj0015-model-server\\resources\\testdata'
 
-def hit_endpoint(method, endpoint, params=None, verbose=False):
+def hit_endpoint(method, endpoint, params=None, verbose=True):
     connection = httplib.HTTPConnection(host, port)
     if not method in ['GET', 'PUT']:
         raise Exception('Can only handle GET and PUT requests')
@@ -32,9 +32,7 @@ def hit_endpoint(method, endpoint, params=None, verbose=False):
     	print(method + ' ' + url + ', status ' + str(resp.status) + ':\n' + resp_str)
     return json.loads(resp_str)
 
-#hit_endpoint('GET', '/')
-#hit_endpoint('GET', '/models')
-#hit_endpoint('PUT', '/bounce_back', {'par1': 'ghij'})
+hit_endpoint('GET', '/restart')
 resp = hit_endpoint('PUT', '/models/ilastik/pixel_classification/load/', {'project_file': 'demo_px.ilp'})
 pxmid = resp['model_id']
 resp = hit_endpoint('GET', '/models', verbose=True)
@@ -45,4 +43,14 @@ infer_params = {
 	'channel': 0
 	}
 
-hit_endpoint('PUT', '/infer/from_image_file', infer_params)
\ No newline at end of file
+hit_endpoint('PUT', '/infer/from_image_file', infer_params)
+
+import time
+ 
+dt_arr = []
+for i in range(0, 10):
+	t0 = time()
+	time.sleep(0.1)
+	dt_arr.append(time() - t0)	
+print(dt_arr)
+print('mean [s]': sum(dt_arr)/len(dt_arr))

simulate_automic.py

+from multiprocessing import Process
+import os
+import requests
+import unittest
+
+import uvicorn
+
+import conf.server
+
+# run server in subprocess
+
+host = '127.0.0.1'
+port = 5000
+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()
+
+# configure and validate folders etc.
+paths = conf.server.paths
+paths['automic_watch_folder'] = paths['images']['inbound']
+paths['test_source_files'] = ''
+
+# load models by API
+
+# prompt user start AutoMic loop
+
+# move files from one folder to another
+def copy_one_input_image_files(copy=True):
+    pattern = ''
+    os.listdir(paths['test_source_files'])
+
+    # order by increaseing alpha order?  timestamp?
+
+
+    if copy:
+        # copy image from test source files to automic watch folder
+    else:
+        # move them
+
+    # recursive repeat until nothign is left
+
+# point to server session logs
+
+
+# shut down server
+server_process.terminate()
+
+
+# do something with the data?
+

tests/test_ilastik.py

@@ -152,3 +152,21 @@ class TestIlastikOverApi(TestServerBaseClass):
             },
         )
         self.assertEqual(resp_infer.status_code, 200, resp_infer.content.decode())
+
+    def test_load_ilastik_pixel_model_in_subdirectory(self):
+        px_ilp = 'proj0011-exp0004/px3d.ilp'
+        pf = px_ilp
+
+        resp_load = requests.put(
+            self.uri + 'models/ilastik/pixel_classification/load/',
+            params={'project_file': pf},
+        )
+        model_id = resp_load.json()['model_id']
+
+        self.assertEqual(resp_load.status_code, 200, resp_load.json())
+        resp_list = requests.get(self.uri + 'models')
+        self.assertEqual(resp_list.status_code, 200)
+        rj = resp_list.json()
+        self.assertEqual(rj[model_id]['class'], 'IlastikPixelClassifierModel')
+
+        return model_id