Merge branch 'master' of https://github.com/IITM-DONLAB/python-dnn

Author: sudhargk

setup.py

@@ -0,0 +1,144 @@
+#!/usr/bin/env python
+"""
+python-dnn uses python (and theano) to implement major Deep Learing Networks.
+It currently supports:
+        CNN
+        SDA
+        DBN
+        A general DNN Finetune kit with maxout and dropout.
+"""
+
+from setuptools import setup, find_packages,Command
+import subprocess
+import os 
+
+
+DOCLINES = __doc__.split("\n")
+
+
+CLASSIFIERS = """\
+Development Status :: 4 - Beta
+Intended Audience :: Science/Research
+Intended Audience :: Developers
+License :: Apache v2.0 License
+Programming Language :: C
+Programming Language :: Python
+Topic :: Software Development
+Topic :: Scientific/Engineering
+Operating System :: POSIX
+
+"""
+
+MAJOR = 1
+MINOR = 0
+MICRO = 1
+ISRELEASED = True
+VERSION = '%d.%d.%d' % (MAJOR, MINOR, MICRO)
+
+
+
+
+class CleanCommand(Command):
+    """Custom clean command to tidy up the project root."""
+    user_options = []
+    def initialize_options(self):
+        pass
+    def finalize_options(self):
+        pass
+    def run(self):
+        os.system('rm -vrf ./build ./dist ./*.pyc ./*.tgz ./*.egg-info ./src/pythonDnn/version.py ./src/*.egg-info')
+
+
+# Return the git revision as a string
+def git_version():
+    def _minimal_ext_cmd(cmd):
+        # construct minimal environment
+        env = {}
+        for k in ['SYSTEMROOT', 'PATH']:
+            v = os.environ.get(k)
+            if v is not None:
+                env[k] = v
+        env['LANGUAGE'] = 'C'
+        env['LANG'] = 'C'
+        env['LC_ALL'] = 'C'
+        out = subprocess.Popen(cmd, stdout = subprocess.PIPE, env=env).communicate()[0]
+        return out
+
+    try:
+    	out = _minimal_ext_cmd(['git', 'rev-parse', 'HEAD'])
+    	GIT_REVISION = out.strip().decode('ascii')
+    except OSError:
+    	GIT_REVISION = "Unknown"
+
+    return GIT_REVISION
+
+
+def get_version_info():
+    # Adding the git rev number needs to be done inside
+    # write_version_py(), otherwise the import of scipy.version messes
+    # up the build under Python 3.
+    FULLVERSION = VERSION
+    if os.path.exists('.git'):
+        GIT_REVISION = git_version()
+    else:
+        GIT_REVISION = "Unknown"
+
+    if not ISRELEASED:
+        FULLVERSION += '.dev-' + GIT_REVISION[:7]
+
+    return FULLVERSION, GIT_REVISION
+
+
+def write_version_py(filename='src/pythonDnn/version.py'):
+    cnt = """
+# THIS FILE IS GENERATED FROM SCIPY SETUP.PY
+short_version = '%(version)s'
+version = '%(version)s'
+full_version = '%(full_version)s'
+git_revision = '%(git_revision)s'
+release = %(isrelease)s
+
+if not release:
+    version = full_version
+"""
+    FULLVERSION, GIT_REVISION = get_version_info()
+
+    a = open(filename, 'w')
+    try:
+        a.write(cnt % {'version': VERSION,
+                       'full_version' : FULLVERSION,
+                       'git_revision' : GIT_REVISION,
+                       'isrelease': str(ISRELEASED)})
+    finally:
+        a.close()
+
+if __name__ == '__main__':
+    # Rewrite the version file every time
+    write_version_py()
+
+    try:
+        import theano
+        requires=[]
+    except ImportError:
+        requires=['theano>=0.7.0']
+
+    metadata = dict(
+        name = 'pythonDnn',
+        maintainer = "pythonDnn",
+        maintainer_email = "pythonDnn@ex.org",
+        description = DOCLINES[0],
+        long_description = "\n".join(DOCLINES[2:]),
+        url = "https://github.com/IITM-DONLAB/python-dnn",
+        download_url = "https://github.com/IITM-DONLAB/python-dnn/zipball/master",
+        license = 'Apache v2.0 License',
+        packages = [ 
+        	'pythonDnn.io_modules', 'pythonDnn.layers', 'pythonDnn.models',
+        	'pythonDnn.run', 'pythonDnn.utils'],
+        package_dir = {'': 'src'},
+        install_requires = requires,
+        zip_safe=False,
+        cmdclass={'clean': CleanCommand,},
+    )
+    FULLVERSION, GIT_REVISION = get_version_info()
+    metadata['version'] = FULLVERSION
+    setup(**metadata)

src/main.py

@@ -17,12 +17,12 @@
 
 
 
-from utils.load_conf import load_model
+from pythonDnn.utils.load_conf import load_model
 import sys
 
 import logging
 logger = logging.getLogger(__name__)
-from io_modules import setLogger
+from pythonDnn.io_modules import setLogger
 
 
 def setLoggerLevel(modelConfig,name=None):
@@ -49,15 +49,15 @@ def runNet(modelConfig):
 	nnetType = modelConfig ['nnetType']
 	logger.info("Loading Other Configuration for %s",nnetType);
 	if nnetType == 'CNN':
-		from run.run_CNN import runCNN as runModel
+		from pythonDnn.run.run_CNN import runCNN as runModel
 	elif nnetType == 'CNN3D':
-		from run.run_CNN3d import runCNN3D as runModel
+		from pythonDnn.run.run_CNN3d import runCNN3D as runModel
 	elif nnetType == 'RBM':
-		from run.run_DBN import runRBM as runModel
+		from pythonDnn.run.run_DBN import runRBM as runModel
 	elif nnetType == 'SDA':
-		from run.run_SDA import runSdA as runModel
+		from pythonDnn.run.run_SDA import runSdA as runModel
 	elif nnetType == 'DNN':
-		from run.run_DNN import runDNN as runModel
+		from pythonDnn.run.run_DNN import runDNN as runModel
 	else :
 		logger.error('Unknown nnet Type')
 		return 1

src/pythonDnn/__init__.py

@@ -0,0 +1 @@
+

src/io_modules/__init__.py src/pythonDnn/io_modules/__init__.pysrc/io_modules/__init__.py renamed to src/pythonDnn/io_modules/__init__.py

@@ -2,10 +2,10 @@
 import theano
 import theano.tensor as T
 
-from utils.utils import dimshuffle
-from io_modules.file_writer import write_dataset
-from io_modules.file_reader import read_dataset
-from io_modules import create_folder_structure_if_not_exists
+from pythonDnn.utils.utils import dimshuffle
+from pythonDnn.io_modules.file_writer import write_dataset
+from pythonDnn.io_modules.file_reader import read_dataset
+from pythonDnn.io_modules import create_folder_structure_if_not_exists
 
 import logging
 logger = logging.getLogger(__name__)

src/io_modules/data_exporter.py src/pythonDnn/io_modules/data_exporter.pysrc/io_modules/data_exporter.py renamed to src/pythonDnn/io_modules/data_exporter.py

@@ -1,7 +1,7 @@
 import json,numpy,sys,os
 import theano
 import theano.tensor as T
-from utils.utils import dimshuffle
+from pythonDnn.utils.utils import dimshuffle
 
 import logging
 logger = logging.getLogger(__name__)
@@ -503,6 +503,8 @@ def read_file_info(self):
 		self.header['featdim'] = self.feat_dim
 		self.header['classes'] = self.classes
 
+		self.childhandles = [None for i in xrange(self.classes)]
+
 		logger.debug('T2 Filereader : feat : %d' % self.feat_dim)
 
 		#load filehandle for all classes
@@ -521,6 +523,7 @@ def read_file_info(self):
 		batch_size = self.batch_size
 		self.setPartitionFrames()
 
+		#logger.critical(str(self.last_class_idx))
 
 		if self.frames_per_partition < self.classes:
 			logger.critical('Number of frames per partition must be greater than the number of classes,'
@@ -538,12 +541,12 @@ def read_next_partition_data(self,already_read=0,pad_zeros=False,makeShared=True
 		while cur_frame_num < self.frames_per_partition and none_cnt < self.classes :
 			if self.childhandles[self.last_class_idx] is None:	
 				#if the child handle is not initialized
-				data_file = self.filenames[self.last_class_idx][fileIndex[self.last_class_idx]];
+				data_file = self.filenames[self.last_class_idx][self.fileIndex[self.last_class_idx]];
 				##Get Next Filename in last Class.
 				if data_file != None:
 					#if Next Filename == NULL;
 
-					fileIndex[self.last_class_idx] = fileIndex[self.last_class_idx] + 1;
+					self.fileIndex[self.last_class_idx] = self.fileIndex[self.last_class_idx] + 1;
 					child_options = self.options.copy()
 					child_options['filename']=data_file
 					child_options['label']= self.last_class_idx

src/io_modules/db_io.py src/pythonDnn/io_modules/db_io.pysrc/io_modules/db_io.py renamed to src/pythonDnn/io_modules/db_io.py

@@ -1,6 +1,6 @@
 
 import json,numpy,os
-from io_modules import create_folder_structure_if_not_exists
+from pythonDnn.io_modules import create_folder_structure_if_not_exists
 
 import logging
 logger = logging.getLogger(__name__)