ChessAnalysisPipeline 0.0.2__py3-none-any.whl → 0.0.4__py3-none-any.whl

CHAP/tomo/reader.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python  
+
+if __name__ == '__main__':
+    from CHAP.reader import main
+    main()

CHAP/tomo/writer.py

@@ -0,0 +1,5 @@
+#!/usr/bin/env python  
+
+if __name__ == '__main__':
+    from CHAP.writer import main
+    main()

CHAP/writer.py

@@ -52,177 +52,27 @@ class Writer():
             file.write(data)
         return(data)
 
-class YAMLWriter(Writer):
-    def _write(self, data, filename, force_overwrite=False):
-        '''If `data` is a `dict`, write it to `filename`.
-
-        :param data: the dictionary to write to `filename`.
-        :type data: dict
-        :param filename: name of the file to write to.
-        :type filename: str
-        :param force_overwrite: flag to allow data in `filename` to be
-            overwritten if it already exists.
-        :type force_overwrite: bool
-        :raises TypeError: if `data` is not a `dict`
-        :raises RuntimeError: if `filename` already exists and
-            `force_overwrite` is `False`.
-        :return: the original input data
-        :rtype: dict
-        '''
-
-        import yaml
-
-        if not isinstance(data, (dict, list)):
-            raise(TypeError(f'{self.__name__}.write: input data must be a dict or list.'))
-
-        if not force_overwrite:
-            if os.path.isfile(filename):
-                raise(RuntimeError(f'{self.__name__}: {filename} already exists.'))
-
-        with open(filename, 'w') as outf:
-            yaml.dump(data, outf, sort_keys=False)
-
-        return(data)
-
-class ExtractArchiveWriter(Writer):
-    def _write(self, data, filename):
-        '''Take a .tar archive represented as bytes in `data` and write the
-        extracted archive to files.
-
-        :param data: the archive data
-        :type data: bytes
-        :param filename: the name of a directory to which the archive files will
-            be written
-        :type filename: str
-        :return: the original `data`
-        :rtype: bytes
-        '''
-
-        from io import BytesIO
-        import tarfile
-
-        tar = tarfile.open(fileobj=BytesIO(data))
-        tar.extractall(path=filename)
-
-        return(data)
-
-
-class NexusWriter(Writer):
-    def _write(self, data, filename, force_overwrite=False):
-        '''Write `data` to a NeXus file
-
-        :param data: the data to write to `filename`.
-        :param filename: name of the file to write to.
-        :param force_overwrite: flag to allow data in `filename` to be
-            overwritten, if it already exists. 
-        :return: the original input data
-        '''
-
-        from nexusformat.nexus import NXobject
-        import xarray as xr
-        
-        if isinstance(data, NXobject):
-            nxstructure = data
-
-        elif isinstance(data, xr.Dataset):
-            nxstructure = self.get_nxdata_from_dataset(data)
-
-        elif isinstance(data, xr.DataArray):
-            nxstructure = self.get_nxdata_from_dataarray(data)
-        
-        else:
-            raise(TypeError(f'{self.__name__}.write: unknown data format: {type(data).__name__}'))
-
-        mode = 'w' if force_overwrite else 'w-'
-        nxstructure.save(filename, mode=mode)
-
-        return(data)
-
-
-    def get_nxdata_from_dataset(self, dset):
-        '''Return an instance of `nexusformat.nexus.NXdata` that represents the
-        data and metadata attributes contained in `dset`.
-
-        :param dset: the input dataset to represent
-        :type data: xarray.Dataset
-        :return: `dset` represented as an instance of `nexusformat.nexus.NXdata`
-        :rtype: nexusformat.nexus.NXdata
-        '''
-
-        from nexusformat.nexus import NXdata, NXfield
-
-        nxdata_args = {'signal':None, 'axes':()}
-
-        for var in dset.data_vars:
-            data_var = dset[var]
-            nxfield = NXfield(data_var.data,
-                              name=data_var.name,
-                              attrs=data_var.attrs)
-            if nxdata_args['signal'] is None:
-                nxdata_args['signal'] = nxfield
-            else:
-                nxdata_args[var] = nxfield
-
-        for coord in dset.coords:
-            coord_var = dset[coord]
-            nxfield = NXfield(coord_var.data,
-                              name=coord_var.name,
-                              attrs=coord_var.attrs)
-            nxdata_args['axes'] = (*nxdata_args['axes'], nxfield)
-
-        nxdata = NXdata(**nxdata_args)
-        nxdata.attrs['xarray_attrs'] = json.dumps(dset.attrs)
-
-        return(nxdata)
-
-    def get_nxdata_from_dataarray(self, darr):
-        '''Return an instance of `nexusformat.nexus.NXdata` that represents the
-        data and metadata attributes contained in `darr`.
-
-        :param darr: the input dataset to represent
-        :type darr: xarray.DataArray
-        :return: `darr` represented as an instance of `nexusformat.nexus.NXdata`
-        :rtype: nexusformat.nexus.NXdata
-        '''
-
-        from nexusformat.nexus import NXdata, NXfield
-
-        nxdata_args = {'signal':None, 'axes':()}
-
-        nxdata_args['signal'] = NXfield(darr.data,
-                                        name=darr.name,
-                                        attrs=darr.attrs)
-
-
-        for coord in darr.coords:
-            coord_var = darr[coord]
-            nxfield = NXfield(coord_var.data,
-                              name=coord_var.name,
-                              attrs=coord_var.attrs)
-            nxdata_args['axes'] = (*nxdata_args['axes'], nxfield)
-
-        nxdata = NXdata(**nxdata_args)
-        nxdata.attrs['xarray_attrs'] = json.dumps(darr.attrs)
-
-        return(nxdata)
-
-
 class OptionParser():
-    '''User based option parser'''
-    def __init__(self):
-        self.parser = argparse.ArgumentParser(prog='PROG')
-        self.parser.add_argument("--data", action="store",
-            dest="data", default="", help="Input data")
-        self.parser.add_argument("--filename", action="store",
-            dest="filename", default="", help="Output file")
-        self.parser.add_argument("--writer", action="store",
-            dest="writer", default="Writer", help="Writer class name")
-        self.parser.add_argument('--log-level', choices=logging._nameToLevel.keys(),
+        '''User based option parser'''
+        def __init__(self):
+            self.parser = argparse.ArgumentParser(prog='PROG')
+            self.parser.add_argument(
+                '--data', action='store',
+                dest='data', default='', help='Input data')
+            self.parser.add_argument(
+                '--filename', action='store',
+                        dest='filename', default='', help='Output file')
+            self.parser.add_argument(
+                '--writer', action='store',
+                dest='writer', default='Writer', help='Writer class name')
+            self.parser.add_argument(
+                '--log-level', choices=logging._nameToLevel.keys(),
             dest='log_level', default='INFO', help='logging level')
 
-def main():
+def main(opt_parser=OptionParser):
     '''Main function'''
-    optmgr  = OptionParser()
+
+    optmgr  = opt_parser()
     opts = optmgr.parser.parse_args()
     clsName = opts.writer
     try:

{ChessAnalysisPipeline-0.0.2.dist-info → ChessAnalysisPipeline-0.0.4.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ChessAnalysisPipeline
-Version: 0.0.2
+Version: 0.0.4
 Summary: CHESS analysis pipeline framework
 Home-page: https://github.com/CHESSComputing/ChessAnalysisPipeline
 Author: Keara Soloway, Rolf Verberg, Valentin Kuznetsov

ChessAnalysisPipeline-0.0.4.dist-info/RECORD

@@ -0,0 +1,50 @@
+CHAP/__init__.py,sha256=t3gMEDUIChA7W1XF2zJTisA4hoF2WijDO_EJLlV2EYo,99
+CHAP/pipeline.py,sha256=bmPFPlzmU7GvRa5KBd5zo6u_Rk9qtkG5tgiRvpfwcxg,2156
+CHAP/processor.py,sha256=j3GOvwQufL37gt2YKe2c8tZjEH2OtEUDRkgHpu26dck,4247
+CHAP/reader.py,sha256=12Xn78J06KJ5wzGnCZKSiak8irCtOVX2wtxV7eH3Pb0,3577
+CHAP/runner.py,sha256=MA0Q3KTAnPnw25i1L7XPs4ZkszfRfByD_qBshsokL2A,2412
+CHAP/writer.py,sha256=tDeQIEgTm-p8zH0g8EmqFTiGBFRM_A_Q9PyBjE1vaac,2759
+CHAP/common/__init__.py,sha256=cnkVDvaf3NhnmBAzwuUFpotYv9VWxOVhKwqE0qZLbNQ,991
+CHAP/common/processor.py,sha256=sEiSFqXhskrKVV6BDwGFwWpbAJ0aV1JXz2BO1l3oql4,24425
+CHAP/common/reader.py,sha256=DqKRLfG5PLf2aj039aV2FIN5ZmhR7XkZ6EyPDSLUZqY,3547
+CHAP/common/writer.py,sha256=HwMMCVldjQGb3HK9ysfdyfkUplnrdZjyqHnon0ne3DU,2910
+CHAP/common/models/__init__.py,sha256=wkCmQ08zciMzjbQVBjKZacSPUGICqTFcfJ3VaWYBtNY,106
+CHAP/common/models/integration.py,sha256=q18QpPtI7iLd1Asj3NnKbHmB5YIlLm9crKPmtLT37c0,25169
+CHAP/common/models/map.py,sha256=OXtXhohGrKrPCgkvxrweSDxnYpJf39KXxvvYsE5JBTo,25035
+CHAP/common/utils/__init__.py,sha256=lDyThufb9FjaqtUnZ7vDEyaF0r9S5Wo5Ty4qkjYNZRY,1497
+CHAP/common/utils/fit.py,sha256=-nOPfd6yUnUDNyLjLGJVxOp0ET4fKD-Bwh5C_bLx8bY,127303
+CHAP/common/utils/general.py,sha256=VkGFECXdbB2NicOt9iGhpIJPdvGPc6eHdtiaiqzDM1A,48178
+CHAP/common/utils/material.py,sha256=KQfORTqLbp8p9pWeSYD6mYzzpYncIEfbHVPiZ5E1PrA,10472
+CHAP/common/utils/scanparsers.py,sha256=ZxFgMQrD98vTjXbkqPXpA_xjWhL7Gk0cIBD0mvf67GQ,34386
+CHAP/edd/__init__.py,sha256=0POOQcuL72QQJghdN9LfYHNZCHdAOjYaLYg2ebr_URo,262
+CHAP/edd/models.py,sha256=E3gUBI0bgnR_GoLJE5XkY8bOWs7z44dcK0QaqqP0vXU,8448
+CHAP/edd/processor.py,sha256=AjI9CZyzBDgBNzKb72n1sc_dkH60LY0h5SyXTkTPbUo,13557
+CHAP/edd/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
+CHAP/edd/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
+CHAP/inference/__init__.py,sha256=huci54T9WyoORENtAO-Wq7qdKfQvh8ocaRwOAoov2fo,129
+CHAP/inference/processor.py,sha256=Sl317ovfhAQPeThOe3Es6soHxH-ckusFiX9GPqxhfMw,2648
+CHAP/inference/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
+CHAP/inference/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
+CHAP/saxswaxs/__init__.py,sha256=aVB0vCzeQYr7sQfodr_qE9896aErCY-wcVf2hGoW-vs,196
+CHAP/saxswaxs/processor.py,sha256=C8BXfAvPqoNR_Xpk9CmDOiWY3ZhW4E32SJ2jY3N5WgU,99
+CHAP/saxswaxs/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
+CHAP/saxswaxs/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
+CHAP/sin2psi/__init__.py,sha256=tYTpc0_bhJ9zCwwaILtkekLR7R3SxzkynugY6D3djnE,243
+CHAP/sin2psi/processor.py,sha256=C8BXfAvPqoNR_Xpk9CmDOiWY3ZhW4E32SJ2jY3N5WgU,99
+CHAP/sin2psi/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
+CHAP/sin2psi/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
+CHAP/tomo/__init__.py,sha256=cFq3uemguYhC3y2hKAO60Omoll5p8mWBHdCrCjBWfCA,150
+CHAP/tomo/models.py,sha256=8-sFRVfbMyy-R0p3HdNaJXH1K9YKDgb4JEXehPYuRns,4857
+CHAP/tomo/processor.py,sha256=_TILlIyM4-dy18CTmqJ0xF-MR0x3RKwppW1mt_dcqV0,97527
+CHAP/tomo/reader.py,sha256=md3gt82kjNOR3mMjcsCfqbmWLuPhl6JA6Qk1ek9tItA,96
+CHAP/tomo/writer.py,sha256=jQGikOjYx7-MURPqMkDqYw8sig2HauGulUlH1nf-jvY,96
+MLaaS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+MLaaS/ktrain.py,sha256=SPDUOQgjBDSx7sI8vZNXog9orvSyKmzpe6TdGHol9qM,7467
+MLaaS/mnist_img.py,sha256=ppDtlo6yrNQy0oIhFZVOnLvHJrR3ZPZ3PjZTtJY8l0E,2738
+MLaaS/tfaas_client.py,sha256=zpZ201wwcQBW1XkzDakD9Kl_NRSESAUdbnN6k6Ey15A,14889
+ChessAnalysisPipeline-0.0.4.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
+ChessAnalysisPipeline-0.0.4.dist-info/METADATA,sha256=KzNtqjPNZkHL92ukFXnF96tA2wv8xvEL5XDKdp-XafM,1219
+ChessAnalysisPipeline-0.0.4.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
+ChessAnalysisPipeline-0.0.4.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
+ChessAnalysisPipeline-0.0.4.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
+ChessAnalysisPipeline-0.0.4.dist-info/RECORD,,

CHAP/async.py

@@ -1,56 +0,0 @@
-#!/usr/bin/env python
-#-*- coding: utf-8 -*-
-#pylint: disable=
-"""
-File       : async.py
-Author     : Valentin Kuznetsov <vkuznet AT gmail dot com>
-Description: AsyncProcessor module
-"""
-
-# system modules
-import asyncio
-
-# local modules
-from CHAP.processor import Processor, PrintProcessor
-
-
-async def task(mgr, doc):
-    """
-    Process given data using provided task manager
-    """
-    return mgr.process(doc)
-
-
-async def executeTasks(mgr, docs):
-    """
-    Process given set of documents using provided task manager
-    """
-    coRoutines = [task(mgr, d) for d in docs]
-    await asyncio.gather(*coRoutines)
-
-
-class AsyncProcessor(Processor):
-    """
-    AsyncProcesor process given data via asyncio module
-    """
-    def __init__(self, mgr):
-        super().__init__()
-        self.mgr = mgr
-
-    def _process(self, docs):
-        """
-        Internal method to process given data documents
-        """
-        asyncio.run(executeTasks(self.mgr, docs))
-
-def example():
-    """
-    Helper function to demonstrate usage of AsyncProcessor
-    """
-    docs = [1,2,3]
-    mgr = PrintProcessor()
-    processor = AsyncProcessor(mgr)
-    processor.process(docs)
-
-if __name__ == '__main__':
-    example()

ChessAnalysisPipeline-0.0.2.dist-info/RECORD

@@ -1,17 +0,0 @@
-CHAP/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-CHAP/async.py,sha256=VSfC0fv339SgRYGwhZ2ChYpZC3flkD1zs3JdpBqpoko,1203
-CHAP/pipeline.py,sha256=S_o6Kw3vz-tgLPSF-CSSzsQSyASlR3spALHP3YATqkQ,2158
-CHAP/processor.py,sha256=CzcuMSKWzJ6GsI12euarvjcHJ-bW-GsrtCPQJllxC4w,38795
-CHAP/reader.py,sha256=uuZlBqfehhnRzHl_H0C0_1u8rzaVpMs2Wq0dKpor-V0,6664
-CHAP/runner.py,sha256=MA0Q3KTAnPnw25i1L7XPs4ZkszfRfByD_qBshsokL2A,2412
-CHAP/writer.py,sha256=P8jEFuJgHLwDBNd5qvPLce5w0hH-Rzroj39vru3G7l4,7788
-MLaaS/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-MLaaS/ktrain.py,sha256=SPDUOQgjBDSx7sI8vZNXog9orvSyKmzpe6TdGHol9qM,7467
-MLaaS/mnist_img.py,sha256=ppDtlo6yrNQy0oIhFZVOnLvHJrR3ZPZ3PjZTtJY8l0E,2738
-MLaaS/tfaas_client.py,sha256=zpZ201wwcQBW1XkzDakD9Kl_NRSESAUdbnN6k6Ey15A,14889
-ChessAnalysisPipeline-0.0.2.dist-info/LICENSE,sha256=GrJL25aZivxje_x-zBbeWASvdmgztxv8kBMhIP4XSMo,1075
-ChessAnalysisPipeline-0.0.2.dist-info/METADATA,sha256=ZCX-n7Cass_Kk6bDslYFmJEu9x62J9AAWbA4ViG6QgI,1219
-ChessAnalysisPipeline-0.0.2.dist-info/WHEEL,sha256=pkctZYzUS4AYVn6dJ-7367OJZivF2e8RA9b_ZBjif18,92
-ChessAnalysisPipeline-0.0.2.dist-info/entry_points.txt,sha256=w-KIKdUjmj5GCobrFC4_jexCsFB4yMXYjrsMWrhI6Co,42
-ChessAnalysisPipeline-0.0.2.dist-info/top_level.txt,sha256=BKhggOWLb9dD6oQm1RXrkJPnXm-zJxVzQef1iXYtt2k,11
-ChessAnalysisPipeline-0.0.2.dist-info/RECORD,,