Client now outside the server repo

clients/imagej/.idea/.gitignore

-# Default ignored files
-/shelf/
-/workspace.xml

clients/imagej/.idea/imagej.iml

-<?xml version="1.0" encoding="UTF-8"?>
-<module type="PYTHON_MODULE" version="4">
-  <component name="NewModuleRootManager">
-    <content url="file://$MODULE_DIR$" />
-    <orderEntry type="inheritedJdk" />
-    <orderEntry type="sourceFolder" forTests="false" />
-  </component>
-</module>
\ No newline at end of file

clients/imagej/.idea/inspectionProfiles/Project_Default.xml

-<component name="InspectionProjectProfileManager">
-  <profile version="1.0">
-    <option name="myName" value="Project Default" />
-    <inspection_tool class="PyUnresolvedReferencesInspection" enabled="true" level="WARNING" enabled_by_default="true">
-      <option name="ignoredIdentifiers">
-        <list>
-          <option value="requests.models.Response.__getitem__" />
-        </list>
-      </option>
-    </inspection_tool>
-  </profile>
-</component>
\ No newline at end of file

clients/imagej/.idea/inspectionProfiles/profiles_settings.xml

-<component name="InspectionProjectProfileManager">
-  <settings>
-    <option name="USE_PROJECT_PROFILE" value="false" />
-    <version value="1.0" />
-  </settings>
-</component>
\ No newline at end of file

clients/imagej/.idea/misc.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectRootManager" version="2" project-jdk-name="Python 2.7 (2)" project-jdk-type="Python SDK" />
-</project>
\ No newline at end of file

clients/imagej/.idea/modules.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ProjectModuleManager">
-    <modules>
-      <module fileurl="file://$PROJECT_DIR$/.idea/imagej.iml" filepath="$PROJECT_DIR$/.idea/imagej.iml" />
-    </modules>
-  </component>
-</project>
\ No newline at end of file

clients/imagej/.idea/vcs.xml

-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$/../.." vcs="Git" />
-  </component>
-</project>
\ No newline at end of file

clients/imagej/client.py

-import httplib
-import json
-import urllib
-
-import sys
-print(sys.version)
-
-HOST = '127.0.0.1'
-PORT = 8000
-uri = 'http://{}:{}/'.format(HOST, PORT)
-
-def hit_endpoint(method, endpoint, params=None, verbose=False):
-    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()
-    if verbose:
-    	print(method + ' ' + url + ', status ' + str(resp.status) + ':\n' + resp_str)
-    return json.loads(resp_str)
-

clients/imagej/example.py

-import os
-import sys
-
-from ij import IJ
-
-# add directory of current script to search path
-scripts_dir = os.path.dirname(sys.argv[0])
-sys.path.append(scripts_dir) 
-
-from ilastik_obmaps import ilastik_map_objects_simple
-
-CHANNEL_TO_ILASTIK = 1 # i.e. index of color channel from confocal stack
-OBJECT_CLASS_FOR_PHOTOACTIVATION = 1
-ROOT = 'c:/Users/rhodes/projects/proj0004-marine-photoactivation/data/exp0021/'
-PIXEL_CLASSIFIER_PATH = ROOT + 'ilastik/px-01.ilp'
-OBJECT_CLASSIFIER_PATH = ROOT + 'ilastik/obj-04.ilp'
-DEBUG = True
-
-#obmap = ilastik_map_objects_simple(
-#    IJ.getImage(),
-#    PIXEL_CLASSIFIER_PATH,
-#    OBJECT_CLASSIFIER_PATH,
-#    CHANNEL_TO_ILASTIK
-#)
-
-# pipeline: remove any existing overlay
-IJ.run("Remove Overlay")
-
-resp = hit_endpoint(
-    'GET',
-    '/ilastik/pixel_then_object_classification/infer',
-    {
-        'px_model_id': id_px_mod,
-        'ob_model_id': id_ob_mod,
-        'input_filename': basename(abspath),
-        'channel': channel,
-    }
-)
-
-
-imp_czi = IJ.getImage()
-#czi_fn = imp_czi.getTitle()
-#czi_desc = czi_fn.split('.')[0]
-#imp_czi.setDisplayMode(IJ.GRAYSCALE)
-IJ.run("Make Subset...", "channels=" + str(CHANNEL_TO_ILASTIK))
-imp_to_ilastik = IJ.getImage()
-
-#obmap = ilastik_map_objects_simple(
-#    imp_to_ilastik,
-#    PIXEL_CLASSIFIER_PATH,
-#    OBJECT_CLASSIFIER_PATH,
-#    CHANNEL_TO_ILASTIK
-#)

clients/imagej/ilastik_obmaps.py

-from client import hit_endpoint
-from os.path import basename, dirname
-
-from ij import IJ
-from ij import ImagePlus
-
-def setup(where, px_ilp):
-    # configure input and output paths
-    resp = hit_endpoint(
-        'PUT',
-        '/paths/watch_input',
-        {
-            'path': where,
-        }
-    )
-    assert resp.status_code == 200, 'Error setting up image directory'
-    resp = hit_endpoint(
-        'PUT',
-        '/paths/watch_output',
-        {
-            'path': where,
-        }
-    )
-    assert resp.status_code == 200, 'Error setting up image directory'
-
-    # load pixel classifier
-    resp = hit_endpoint(
-        'PUT',
-        '/ilastik/pixel_classification/load/',
-        {
-            'project_file': px_ilp,
-            'duplicate': False,
-        },
-    )
-    assert resp.status_code == 200, 'Error loading pixel classifier: ' + {px_ilp}
-    return resp['model_id']
-
-
-def ilastik_map_objects_simple(imp, px_ilp, ob_ilp, channel):
-    """
-
-    :param pixel_classifier: (str)
-    :param object_classifier: (str)
-    :return: ImagePlus
-    """
-    # get info from input ImagePlus
-    abspath = imp.getProp('Location')
-
-    # assert imp is not z-stack
-    id_px_mod = setup(dirname(abspath), px_ilp)
-
-    # load object classifier
-    resp = hit_endpoint(
-        'PUT', '/ilastik/pxmap_to_obj/load/',
-        {
-            'project_file': ob_ilp,
-            'duplicate': False,
-        },
-    )
-    assert resp.status_code == 200, 'Error loading object classifier: ' + {ob_ilp}
-    id_ob_mod = resp['model_id']
-
-    # run inference
-    resp = hit_endpoint(
-        'PUT',
-        '/ilastik/pixel_then_object_classification/infer',
-        {
-            'px_model_id': id_px_mod,
-            'ob_model_id': id_ob_mod,
-            'input_filename': basename(abspath),
-            'channel': channel,
-        }
-    )
-    assert resp.status_code == 200, 'Error calling workfow'
-    obmap = resp.json()['object_map_filepath']
-
-    return obmap # obviously need imp
-
-def ilastik_map_objects_with_zmask(imp, px_ilp, ob_ilp, pxmap_threshold, pxmap_foreground_channel, segmentation_channel, patches_channel, zmask_filters):
-    """
-
-    :param pixel_classifier: (str)
-    :param object_classifier: (str)
-    :return: ImagePlus
-    """
-    # get info from input ImagePlus
-    abspath = imp.getProp('Location')
-
-    # assert imp is not z-stack
-    id_px_mod = setup(dirname(abspath), px_ilp)
-
-    # load object classifier
-    resp = hit_endpoint(
-        'PUT', '/ilastik/seg_to_obj/load/',
-        {
-            'project_file': ob_ilp,
-            'duplicate': False,
-        },
-    )
-    assert resp.status_code == 200, 'Error loading object classifier: ' + {ob_ilp}
-    id_ob_mod = resp['model_id']
-
-    # run inference
-    resp = hit_endpoint(
-        'PUT',
-        '/chaeo/classify_zstack/infer',
-        {
-            'px_model_id': id_px_mod,
-            'ob_model_id': id_ob_mod,
-            'input_filename': basename(abspath),
-            'pxmap_threshold': pxmap_threshold,
-            'pxmap_foreground_channel': pxmap_foreground_channel,
-            'segmentation_channel': segmentation_channel,
-            'patches_channel': patches_channel,
-            'zmask_filters': zmask_filters,
-        }
-    )
-    assert resp.status_code == 200, 'Error calling workfow'
-    obmap = resp.json()['output_path']
-
-    return obmap # obviously need imp

clients/readme.md

-The clients.imagej package tracks client scripts and their dependencies, which are intended to run inside ImageJ's 
-Jython interpreter.
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