Project name change from ray to gala

CMakeLists.txt

@@ -1,5 +1,5 @@
 CMAKE_MINIMUM_REQUIRED(VERSION 2.8)
-project (ray)
+project (gala)
 
 include (ExternalProject)
 
@@ -63,8 +63,8 @@ else ()
     include (scikit-learn)
     include (syngeo)
 
-    # Install ray
-    add_custom_target (ray ALL 
+    # Install gala
+    add_custom_target (gala ALL 
         DEPENDS     ${APP_DEPENDENCIES}
         COMMAND     ${BUILDEM_ENV_STRING} ${PYTHON_EXE} setup.py install
         WORKING_DIRECTORY   ${CMAKE_CURRENT_SOURCE_DIR})

README.md

@@ -1,9 +1,9 @@
-# ray: segmentation of nD images
+# gala: segmentation of nD images
 
-Ray is a python library for performing and evaluating image segmentation,
-distributed under the open-source 
-[MIT license](http://www.opensource.org/licenses/mit-license.php).
-It supports n-dimensional images (images, volumes, videos, videos of 
+Gala is a python library for performing and evaluating image segmentation,
+distributed under the open-source [Janelia Farm license](http://janelia-flyem.github.com/janelia_farm_license.html).
+
+Gala supports n-dimensional images (images, volumes, videos, videos of 
 volumes...) and multiple channels per image.
 
 ## Requirements (tested versions)
@@ -30,10 +30,10 @@ but if you don't install it you can still use SVM or AdaBoost classifiers.
 
 ## Installation
 
-### Installing ray
+### Installing gala
 
-Ray is a python library and can be installed in two ways:
-* Add the ray directory to your PYTHONPATH environment variable
+Gala is a python library and can be installed in two ways:
+* Add the gala directory to your PYTHONPATH environment variable
 * Use setup.py to install it into your preferred python:
 
     % python setup.py install
@@ -46,7 +46,7 @@ download, compile, test, and install requirements into a specified buildem
 prefix directory.  
 
 ```
-% cmake -D BUILDEM_DIR=/path/to/platform-specific/build/dir <ray directory>
+% cmake -D BUILDEM_DIR=/path/to/platform-specific/build/dir <gala directory>
 % make
 ```
 
@@ -56,19 +56,19 @@ using the buildem system.
 ### Testing
 
 The test coverage is rather tiny, but it is still a nice way to check you
-haven't completely screwed up your installation. From the Ray root directory,
-run `python test/test_ray.py` to run some regression tests.
+haven't completely screwed up your installation. From the Gala root directory,
+run `python test/test_gala.py` to run some regression tests.
 
 ## Usage
 
 ### Agglomeration
 
 Suppose you have already trained a pixel level boundary detector, and want to
 perform mean agglomeration on it. This is the simplest form of agglomeration
-and was the initial design spec for Ray. Now:
+and was the initial design spec for Gala. Now:
 
 ```python
-from ray import imio, agglo, morpho
+from gala import imio, agglo, morpho
 # prob is a numpy ndarray
 # probabilities-* can be one file for 2D segmentation, or many files for 3D.
 prob = imio.read_image_stack('probabilities-*.png') 
@@ -111,7 +111,7 @@ These are provided by the `classify` module, and built into the `agglo.Rag`
 class.
 
 ```python
-from ray import classify
+from gala import classify
 gs = imio.read_h5_stack('gold-standard-segmentation.h5')
 fm = classify.MomentsFeatureManager()
 fh = classify.HistogramFeatureManager()
@@ -221,7 +221,7 @@ we have done?
 We can use the `evaluate` submodule to check our performance.
 
 ```python
-from ray import evaluate
+from gala import evaluate
 from scipy.ndimage.measurements import label
 t = imio.read_h5_stack('test-gold-standard.h5')
 s = label(ucm_test < 0.5)[0]
@@ -242,6 +242,6 @@ fm = evaluate.fm_index(s, t)
 pr = evaluate.pixel_wise_precision_recall(s, t)
 ```
 
-That's a quick summary of the capabilities of Ray. There are of course many
+That's a quick summary of the capabilities of Gala. There are of course many
 options under the hood, many of which are undocumented... Feel free to push me
 to update the documentation of your favorite function!

bin/comparestacks

@@ -8,7 +8,7 @@ pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
 from numpy import *
-from ray import imio, morpho, evaluate as ev
+from gala import imio, morpho, evaluate as ev
 from scipy.ndimage import binary_dilation, generate_binary_structure
 import getopt
 import errno

bin/ray-evaluate → bin/gala-evaluate

@@ -24,7 +24,7 @@ except ImportError:
 from scipy.ndimage import label
 
 # local modules
-from ray import imio, agglo, morpho, evaluate as ev
+from gala import imio, agglo, morpho, evaluate as ev
 
 if __name__ == '__main__':
 

bin/ray-pixel → bin/gala-pixel

@@ -9,5 +9,5 @@ this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
-from ray import pixel
+from gala import pixel
 sys.exit(pixel.entrypoint(sys.argv))

bin/ray-remove-inclusions → bin/gala-remove-inclusions

@@ -9,7 +9,7 @@ this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
-from ray import imio, agglo
+from gala import imio, agglo
 import argparse
 import logging
 
@@ -24,7 +24,7 @@ def main(argv):
         dest='output_name', default='./raveler-export')
     args = parser.parse_args()
 
-    MasterLogger = logging.getLogger('ray-reresegment')
+    MasterLogger = logging.getLogger('gala-reresegment')
     MasterLogger.propagate = False
     MasterLogger.setLevel(logging.DEBUG)
     console = logging.StreamHandler(sys.stdout)

bin/ray-segment → bin/gala-segment

@@ -31,10 +31,10 @@ except ImportError:
                                         'Synapse-aware mode not available.')
 
 # local modules
-from ray import imio, agglo, morpho, classify, features
+from gala import imio, agglo, morpho, classify, features
 
 try:
-    from ray import stack_np
+    from gala import stack_np
 except ImportError:
     pass
 
@@ -125,7 +125,7 @@ if __name__ == '__main__':
 
     if args.use_neuroproof:
         try:
-            from ray import stack_np
+            from gala import stack_np
         except ImportError:
             MasterLogger.warning("NeuroProof could not be imported")
             sys.exit(1)
@@ -149,7 +149,7 @@ if __name__ == '__main__':
         MasterLogger.error("Experiment name cannot be a path")
         sys.exit(1)
 
-    prim = logging.FileHandler(experiment_prefix + ".ray-segment.log", 'a')
+    prim = logging.FileHandler(experiment_prefix + ".gala-segment.log", 'a')
     prim.setLevel(logging.DEBUG)
     prim.setFormatter(logging.Formatter(
         fmt='%(asctime)s %(levelname)-8s %(message)s',

bin/ray-segmentation-pipeline → bin/gala-segmentation-pipeline

@@ -9,5 +9,5 @@ this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
-from ray import segmentation_pipeline
+from gala import segmentation_pipeline
 sys.exit(segmentation_pipeline.entrypoint(sys.argv))

bin/ray-test-package → bin/gala-test-package

@@ -9,5 +9,5 @@ this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
-from ray import test_package
+from gala import test_package
 sys.exit(test_package.entrypoint(sys.argv))

bin/ray-train → bin/gala-train

@@ -30,7 +30,7 @@ except ImportError:
     logging.warning('Could not import syngeo. Synapse-aware mode not available.')
 
 # local modules
-from ray import imio, agglo, morpho, classify, features, evaluate
+from gala import imio, agglo, morpho, classify, features, evaluate
 
 
 if __name__ == '__main__':
@@ -135,7 +135,7 @@ if __name__ == '__main__':
 
     if args.use_neuroproof:
         try:
-            from ray import stack_np
+            from gala import stack_np
         except ImportError:
             MasterLogger.warning("NeuroProof could not be imported.  sys path: %s" % sys.path)
             raise
@@ -153,7 +153,7 @@ if __name__ == '__main__':
         MasterLogger.error("Experiment name cannot be a path")
         sys.exit(1)
 
-    prim = logging.FileHandler(experiment_prefix + ".ray-train.log", 'a')
+    prim = logging.FileHandler(experiment_prefix + ".gala-train.log", 'a')
     prim.setLevel(logging.DEBUG)
     prim.setFormatter(logging.Formatter(
         fmt='%(asctime)s %(levelname)-8s %(message)s', 

bin/ray-valprob → bin/gala-valprob

@@ -9,5 +9,5 @@ this_dir = os.path.dirname(sys.argv[0])
 pkg_dir = os.path.abspath(os.path.join(this_dir, '..'))
 sys.path.insert(0, pkg_dir)
 
-from ray import valprob
+from gala import valprob
 sys.exit(valprob.entrypoint(sys.argv))

ray/__init__.py → gala/__init__.py

@@ -1,13 +1,13 @@
 """
-Ray
+Gala
 ===
 
-    Ray is a Python package for nD image segmentation. 
+    Gala is a Python package for nD image segmentation. 
 """
 
 import sys, logging
 if sys.version_info[:2] < (2,6):
-    logging.warning('Ray has not been tested on Python versions prior to 2.6'+
+    logging.warning('Gala has not been tested on Python versions prior to 2.6'+
         ' (%d.%d detected).'%sys.version_info[:2])
 
 __author__ = 'Juan Nunez-Iglesias <[email protected]>, '+\

ray/classify.py → gala/classify.py

@@ -132,7 +132,7 @@ def get_classifier(name='random forest', *args, **kwargs):
         return DefaultRandomForest(*args, **kwargs)
     else:
         raise NotImplementedError('Classifier "%s" is either not installed ' +
-            'or not implemented in Ray.')
+            'or not implemented in Gala.')
 
 class DefaultRandomForest(RandomForestClassifier):
     def __init__(self, *args, **kwargs):

ray/segmentation_pipeline.py → gala/segmentation_pipeline.py

@@ -17,7 +17,7 @@
     session_manager, pixel, features
 
 try:
-    from ray import stack_np
+    from gala import stack_np
 except ImportError:
     np_installed = False   
 else:

ray/stitch.py → gala/stitch.py

@@ -8,7 +8,7 @@
 from numpy import zeros, bool, hstack, vstack, newaxis, array, savetxt
 from scipy.ndimage.filters import median_filter, gaussian_filter
 from scipy.ndimage.measurements import label
-from ray import single_arg_read_image_stack
+from gala import single_arg_read_image_stack
 
 class EvalAction(argparse.Action):
     def __call__(parser, namespace, values, option_string=None):

ray/test_package.py → gala/test_package.py

@@ -52,12 +52,12 @@ def testIlastik(self):
 
 class testModules(unittest.TestCase):
     def gen_watershed(self):
-        from ray import imio
+        from gala import imio
         import numpy
         from skimage import morphology as skmorph
         from scipy.ndimage import label
 
-        self.datadir = os.path.abspath(os.path.dirname(sys.modules["ray"].__file__)) + "/testdata/"
+        self.datadir = os.path.abspath(os.path.dirname(sys.modules["gala"].__file__)) + "/testdata/"
 
         prediction = imio.read_image_stack(self.datadir +"pixelprobs.h5",
                 group='/volume/prediction', single_channel=False)
@@ -70,9 +70,9 @@ def gen_watershed(self):
     def testNPRFBuild(self):
         if not np_installed:
             self.assertTrue(np_installed)
-        from ray import stack_np
-        from ray import classify
-        self.datadir = os.path.abspath(os.path.dirname(sys.modules["ray"].__file__)) + "/testdata/"
+        from gala import stack_np
+        from gala import classify
+        self.datadir = os.path.abspath(os.path.dirname(sys.modules["gala"].__file__)) + "/testdata/"
 
         cl = classify.load_classifier(self.datadir + "agglomclassifier_np.rf.h5")
         fm_info = json.loads(str(cl.feature_description))
@@ -87,10 +87,10 @@ def testNPRFBuild(self):
         self.assertEqual(stack.number_of_nodes(), 78)
 
     def testAggloRFBuild(self):
-        from ray import agglo
-        from ray import features
-        from ray import classify
-        self.datadir = os.path.abspath(os.path.dirname(sys.modules["ray"].__file__)) + "/testdata/"
+        from gala import agglo
+        from gala import features
+        from gala import classify
+        self.datadir = os.path.abspath(os.path.dirname(sys.modules["gala"].__file__)) + "/testdata/"
 
         cl = classify.load_classifier(self.datadir + "agglomclassifier.rf.h5")
         fm_info = json.loads(str(cl.feature_description))
@@ -108,7 +108,7 @@ def testAggloRFBuild(self):
     def testNPBuild(self):
         if not np_installed:
             self.assertTrue(np_installed)
-        from ray import stack_np
+        from gala import stack_np
         watershed, boundary, dummy = self.gen_watershed()
         stack = stack_np.Stack(watershed, boundary)
         self.assertEqual(stack.number_of_nodes(), 3629)
@@ -118,7 +118,7 @@ def testNPBuild(self):
         self.assertEqual(stack.number_of_nodes(), 82)
 
     def testAggoBuild(self):
-        from ray import agglo
+        from gala import agglo
         watershed, boundary, dummy = self.gen_watershed()
         stack = agglo.Rag(watershed, boundary, nozeros=True)
         self.assertEqual(stack.number_of_nodes(), 3630)
@@ -133,10 +133,10 @@ def testWatershed(self):
 
 class testFlows(unittest.TestCase):
     def testNPFlow(self):
-        import ray
+        import gala
         if not np_installed:
             self.assertTrue(np_installed)
-        self.datadir = os.path.abspath(os.path.dirname(sys.modules["ray"].__file__)) + "/testdata"
+        self.datadir = os.path.abspath(os.path.dirname(sys.modules["gala"].__file__)) + "/testdata"
         writedir = "/tmp/NPregtest"
 
         if os.path.exists(writedir):
@@ -154,7 +154,7 @@ def testNPFlow(self):
         writefile.write(configstr) 
         writefile.close()
 
-        os.system("ray-segmentation-pipeline " + writedir +  " --config-file " +
+        os.system("gala-segmentation-pipeline " + writedir +  " --config-file " +
                "/tmp/NPregtest/config.json --regression --enable-use-neuroproof >& /dev/null")
 
         log_data = open(self.datadir + "/seg-pipeline-np.log", 'r').read()
@@ -167,8 +167,8 @@ def testNPFlow(self):
                         open("/tmp/NPregtest/.seg-pipeline.log", 'r').read())         
 
     def testRegFlow(self):
-        import ray
-        self.datadir = os.path.abspath(os.path.dirname(sys.modules["ray"].__file__)) + "/testdata"
+        import gala
+        self.datadir = os.path.abspath(os.path.dirname(sys.modules["gala"].__file__)) + "/testdata"
         writedir = "/tmp/regtest"
 
         if os.path.exists(writedir):
@@ -185,7 +185,7 @@ def testRegFlow(self):
         writefile.write(configstr) 
         writefile.close()
 
-        os.system("ray-segmentation-pipeline " + writedir +  " --config-file " +
+        os.system("gala-segmentation-pipeline " + writedir +  " --config-file " +
                 "/tmp/regtest/config.json --regression --disable-use-neuroproof >& /dev/null")
 
         log_data = open(self.datadir + "/seg-pipeline.log", 'r').read()

setup.py

@@ -3,16 +3,16 @@
 
 
 
-setup(name = "ray",
+setup(name = "gala",
     version = "1.0",
-    url = "https://github.com/jni/ray",
-    description = "Ray is a python library for performing and evaluating image segmentation.",
-    long_description = "Ray is a python library for performing and evaluating of image segmentation. It supports n-dimensional images (images, volumes, videos, videos of volumes...) and multiple channels per image.",
+    url = "https://github.com/jni/gala",
+    description = "Gala is a python library for performing and evaluating image segmentation.",
+    long_description = "Gala is a python library for performing and evaluating of image segmentation. It supports n-dimensional images (images, volumes, videos, videos of volumes...) and multiple channels per image.",
     author = "Juan Nunez-Iglesias",
     author_email = '[email protected]',
     license = 'LICENSE.txt',
-    packages = ['ray', 'ray.features'],
-    package_data = {'ray': ['testdata/*.*', 'testdata/original_grayscales/*'] },
+    packages = ['gala', 'gala.features'],
+    package_data = {'gala': ['testdata/*.*', 'testdata/original_grayscales/*'] },
     install_requires = [ ],
-    scripts = ["bin/ray-segmentation-pipeline", "bin/ray-train", "bin/ray-test-package", "bin/ray-pixel", "bin/comparestacks", "bin/ray-valprob"]
+    scripts = ["bin/gala-segmentation-pipeline", "bin/gala-train", "bin/gala-test-package", "bin/gala-pixel", "bin/comparestacks", "bin/gala-valprob"]
 )