From 2a1ef087fbc80e2e08e921581150e9e809facbb9 Mon Sep 17 00:00:00 2001
From: Christopher Rhodes <christopher.rhodes@embl.de>
Date: Thu, 26 Sep 2024 15:07:52 +0200
Subject: [PATCH] Removed demo client for now, since these are not covered by
unit testing
---
model_server/clients/__init__.py | 0
model_server/clients/ilastik_map_objects.py | 80 --------------------
model_server/clients/imagej/__init__.py | 0
model_server/clients/imagej/adapter.py | 82 ---------------------
model_server/clients/util.py | 18 -----
5 files changed, 180 deletions(-)
delete mode 100644 model_server/clients/__init__.py
delete mode 100644 model_server/clients/ilastik_map_objects.py
delete mode 100644 model_server/clients/imagej/__init__.py
delete mode 100644 model_server/clients/imagej/adapter.py
delete mode 100644 model_server/clients/util.py
diff --git a/model_server/clients/__init__.py b/model_server/clients/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/model_server/clients/ilastik_map_objects.py b/model_server/clients/ilastik_map_objects.py
deleted file mode 100644
index c395a31f..00000000
--- a/model_server/clients/ilastik_map_objects.py
+++ /dev/null
@@ -1,80 +0,0 @@
-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 (optional): (int) channel of the input image to process, use all channels if not specified
- :return: (str) absolute path where a new object map is written
- """
-
- where = dirname(in_abspath)
- in_file = basename(in_abspath)
-
- px_ilp = params['pixel_classifier_path']
- ob_ilp = params['object_classifier_path']
- channel = params.get('channel', None)
- mip = params.get('mip', False)
-
- # 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/seg/load/',
- body={
- '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/',
- body={
- '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,
- 'mip': mip,
- }
- )
- assert resp['status'] == 200, 'Error calling workfow'
- return resp['content']['object_map_filepath']
-
diff --git a/model_server/clients/imagej/__init__.py b/model_server/clients/imagej/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/model_server/clients/imagej/adapter.py b/model_server/clients/imagej/adapter.py
deleted file mode 100644
index 237aa7ab..00000000
--- a/model_server/clients/imagej/adapter.py
+++ /dev/null
@@ -1,82 +0,0 @@
-"""
-Functionality needed to run a client request sequence (clients.*.main) in the ImageJ model_server 2.7 script environment
-"""
-
-import httplib
-import json
-import urllib
-
-from ij import IJ
-from ij import ImagePlus
-
-HOST = '127.0.0.1'
-PORT = 6221
-uri = 'http://{}:{}/'.format(HOST, PORT)
-
-def hit_endpoint(method, endpoint, params=None, body=None, drop_none=True):
- """
- 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 that are embedded in client request URL
- :param body: (dict) of parameters that JSON-encoded and attached as payload in request
- :param drop_none: (bool) remove (presumably optional) parameters with value equal to None
- :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')
- k_pop = []
- if drop_none and params is not None:
- for k, v in params.items():
- if v is None:
- k_pop.append(k)
- for ki in k_pop:
- params.pop(ki)
-
- if params:
- url = endpoint + '?' + urllib.urlencode(params)
- else:
- url = endpoint
- connection.request(method, url, body=json.dumps(body))
- 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 verify_server(popup=True):
- try:
- resp = hit_endpoint('GET', '/')
- except Exception as e:
- print(e)
- msg = 'Could not find server at: ' + uri
- IJ.log(msg)
- if popup:
- IJ.error(msg)
- raise e
- return False
- if resp['status'] != 200:
- msg = 'Unknown error verifying server at: ' + uri
- if popup:
- IJ.error(msg)
- raise Exception(msg)
- return False
- else:
- IJ.log('Verified server is online at: ' + uri)
- return True
-
-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
diff --git a/model_server/clients/util.py b/model_server/clients/util.py
deleted file mode 100644
index 423e7380..00000000
--- a/model_server/clients/util.py
+++ /dev/null
@@ -1,18 +0,0 @@
-import requests
-
-def get_client(host='127.0.0.1', port=8000):
- """Return a client wrapper for testing in same model_server 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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