diff --git a/clients/__init__.py b/clients/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/clients/imagej/.idea/.gitignore b/clients/imagej/.idea/.gitignore
deleted file mode 100644
index 26d33521af10bcc7fd8cea344038eaaeb78d0ef5..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/.gitignore
+++ /dev/null
@@ -1,3 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
diff --git a/clients/imagej/.idea/imagej.iml b/clients/imagej/.idea/imagej.iml
deleted file mode 100644
index d0876a78d06ac03b5d78c8dcdb95570281c6f1d6..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/imagej.iml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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
diff --git a/clients/imagej/.idea/inspectionProfiles/Project_Default.xml b/clients/imagej/.idea/inspectionProfiles/Project_Default.xml
deleted file mode 100644
index 4b7439eb893169c8d26bba41b6b1722e5c8fe1a3..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/inspectionProfiles/Project_Default.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<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
diff --git a/clients/imagej/.idea/inspectionProfiles/profiles_settings.xml b/clients/imagej/.idea/inspectionProfiles/profiles_settings.xml
deleted file mode 100644
index 105ce2da2d6447d11dfe32bfb846c3d5b199fc99..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/inspectionProfiles/profiles_settings.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<component name="InspectionProjectProfileManager">
- <settings>
- <option name="USE_PROJECT_PROFILE" value="false" />
- <version value="1.0" />
- </settings>
-</component>
\ No newline at end of file
diff --git a/clients/imagej/.idea/misc.xml b/clients/imagej/.idea/misc.xml
deleted file mode 100644
index 42a3a57d4ad17e847fa7223b338beb87f991ad62..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/misc.xml
+++ /dev/null
@@ -1,4 +0,0 @@
-<?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
diff --git a/clients/imagej/.idea/modules.xml b/clients/imagej/.idea/modules.xml
deleted file mode 100644
index f95153e75e8fc539d4eda20668ee4ddc6221cf6b..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/modules.xml
+++ /dev/null
@@ -1,8 +0,0 @@
-<?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
diff --git a/clients/imagej/.idea/vcs.xml b/clients/imagej/.idea/vcs.xml
deleted file mode 100644
index b2bdec2d71b6a5ce4ae49efc37516809c50e4d5e..0000000000000000000000000000000000000000
--- a/clients/imagej/.idea/vcs.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?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
diff --git a/clients/imagej/__init__.py b/clients/imagej/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/clients/imagej/client.py b/clients/imagej/client.py
deleted file mode 100644
index cd8636beb3316067e358405927ac7544b6f7378b..0000000000000000000000000000000000000000
--- a/clients/imagej/client.py
+++ /dev/null
@@ -1,26 +0,0 @@
-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)
-
diff --git a/clients/imagej/example.py b/clients/imagej/example.py
deleted file mode 100644
index 67a50e33f06c2ddaf497d5708b0dfbf4690a5bfe..0000000000000000000000000000000000000000
--- a/clients/imagej/example.py
+++ /dev/null
@@ -1,53 +0,0 @@
-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
-#)
diff --git a/clients/imagej/ilastik_obmaps.py b/clients/imagej/ilastik_obmaps.py
deleted file mode 100644
index e74102d78283e57005bf551d4002ee1b9474bb3c..0000000000000000000000000000000000000000
--- a/clients/imagej/ilastik_obmaps.py
+++ /dev/null
@@ -1,121 +0,0 @@
-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
diff --git a/clients/readme.md b/clients/readme.md
deleted file mode 100644
index 2c49d8f57339dc141633b62fe67fcc7ffd6f9d6f..0000000000000000000000000000000000000000
--- a/clients/readme.md
+++ /dev/null
@@ -1,2 +0,0 @@
-The clients.imagej package tracks client scripts and their dependencies, which are intended to run inside ImageJ's
-Jython interpreter.
\ No newline at end of file