forked from DiamondLightSource/vdsgen
-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Seperate CLI app and class into two files
- Loading branch information
Showing
4 changed files
with
242 additions
and
228 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,147 @@ | ||
| import unittest | ||
| from pkg_resources import require | ||
|
|
||
| require("mock") | ||
| from mock import MagicMock, patch, call | ||
|
|
||
| from vdsgen import app | ||
|
|
||
| parser_patch_path = "argparse.ArgumentParser" | ||
| app_patch_path = "vdsgen.app" | ||
| VDSGenerator_patch_path = app_patch_path + ".VDSGenerator" | ||
|
|
||
|
|
||
| class ParseArgsTest(unittest.TestCase): | ||
|
|
||
| @patch(parser_patch_path + '.add_mutually_exclusive_group') | ||
| @patch(parser_patch_path + '.add_argument_group') | ||
| @patch(parser_patch_path + '.add_argument') | ||
| @patch(parser_patch_path + '.parse_args', | ||
| return_value=MagicMock(empty=False, files=None)) | ||
| def test_parser(self, parse_mock, add_mock, add_group_mock, | ||
| add_exclusive_group_mock): | ||
| group_mock = add_group_mock.return_value | ||
| exclusive_group_mock = add_exclusive_group_mock.return_value | ||
|
|
||
| args = app.parse_args() | ||
|
|
||
| add_mock.assert_has_calls( | ||
| [call("path", type=str, | ||
| help="Root folder to create VDS in. Also where source " | ||
| "files are searched for if --prefix given."), | ||
| call("-o", "--output", type=str, default=None, dest="output", | ||
| help="Output file name. Default is input file prefix with " | ||
| "vds suffix."), | ||
| call("-e", "--empty", action="store_true", dest="empty", | ||
| help="Make empty VDS pointing to datasets " | ||
| "that don't exist, yet."), | ||
| call("-s", "--stripe_spacing", nargs="?", type=int, default=None, | ||
| dest="stripe_spacing", | ||
| help="Spacing between two stripes in a module."), | ||
| call("-m", "--module_spacing", nargs="?", type=int, default=None, | ||
| dest="module_spacing", | ||
| help="Spacing between two modules."), | ||
| call("--source_node", nargs="?", type=str, default=None, | ||
| dest="source_node", | ||
| help="Data node in source HDF5 files."), | ||
| call("--target_node", nargs="?", type=str, default=None, | ||
| dest="target_node", | ||
| help="Data node in VDS file.")]) | ||
|
|
||
| add_group_mock.assert_called_with() | ||
| group_mock.add_argument.assert_has_calls( | ||
| [call("--frames", type=int, default=1, dest="frames", | ||
| help="Number of frames to combine into VDS."), | ||
| call("--height", type=int, default=256, dest="height", | ||
| help="Height of raw datasets."), | ||
| call("--width", type=int, default=1024, dest="width", | ||
| help="Width of raw datasets."), | ||
| call("--data_type", type=str, default="uint16", dest="data_type", | ||
| help="Data type of raw datasets.")]) | ||
|
|
||
| add_exclusive_group_mock.assert_called_with(required=True) | ||
| exclusive_group_mock.add_argument.assert_has_calls( | ||
| [call("-p", "--prefix", type=str, default=None, dest="prefix", | ||
| help="Prefix of files - e.g 'stripe_' to combine the images " | ||
| "'stripe_1.hdf5', 'stripe_2.hdf5' and 'stripe_3.hdf5' " | ||
| "located at <path>."), | ||
| call("-f", "--files", nargs="*", type=str, default=None, | ||
| dest="files", | ||
| help="Manually define files to combine.")]) | ||
|
|
||
| parse_mock.assert_called_once_with() | ||
| self.assertEqual(parse_mock.return_value, args) | ||
|
|
||
| @patch(parser_patch_path + '.error') | ||
| @patch(parser_patch_path + '.parse_args', | ||
| return_value=MagicMock(empty=True, files=None)) | ||
| def test_empty_and_not_files_then_error(self, parse_mock, error_mock): | ||
|
|
||
| app.parse_args() | ||
|
|
||
| error_mock.assert_called_once_with( | ||
| "To make an empty VDS you must explicitly define --files for the " | ||
| "eventual raw datasets.") | ||
|
|
||
| @patch(parser_patch_path + '.error') | ||
| @patch(parser_patch_path + '.parse_args', | ||
| return_value=MagicMock(empty=True, files=["file"])) | ||
| def test_only_one_file_then_error(self, parse_mock, error_mock): | ||
|
|
||
| app.parse_args() | ||
|
|
||
| error_mock.assert_called_once_with( | ||
| "Must define at least two files to combine.") | ||
|
|
||
|
|
||
| class MainTest(unittest.TestCase): | ||
| @patch(VDSGenerator_patch_path) | ||
| @patch(app_patch_path + '.parse_args', | ||
| return_value=MagicMock( | ||
| path="/test/path", prefix="stripe_", empty=True, | ||
| files=["file1.hdf5", "file2.hdf5"], output="vds", | ||
| frames=3, height=256, width=2048, data_type="int16", | ||
| source_node="data", target_node="full_frame", | ||
| stripe_spacing=3, module_spacing=127)) | ||
| def test_main_empty(self, parse_mock, init_mock): | ||
| gen_mock = init_mock.return_value | ||
| args_mock = parse_mock.return_value | ||
|
|
||
| app.main() | ||
|
|
||
| parse_mock.assert_called_once_with() | ||
| init_mock.assert_called_once_with( | ||
| args_mock.path, | ||
| prefix=args_mock.prefix, files=args_mock.files, | ||
| output=args_mock.output, | ||
| source=dict(frames=args_mock.frames, height=args_mock.height, | ||
| width=args_mock.width, dtype=args_mock.data_type), | ||
| source_node=args_mock.source_node, | ||
| target_node=args_mock.target_node, | ||
| stripe_spacing=args_mock.stripe_spacing, | ||
| module_spacing=args_mock.module_spacing) | ||
|
|
||
| gen_mock.generate_vds.assert_called_once_with() | ||
|
|
||
| @patch(VDSGenerator_patch_path) | ||
| @patch(app_patch_path + '.parse_args', | ||
| return_value=MagicMock( | ||
| path="/test/path", prefix="stripe_", empty=False, | ||
| files=["file1.hdf5", "file2.hdf5"], output="vds", | ||
| frames=3, height=256, width=2048, data_type="int16", | ||
| source_node="data", target_node="full_frame", | ||
| stripe_spacing=3, module_spacing=127)) | ||
| def test_main_not_empty(self, parse_mock, generate_mock): | ||
| args_mock = parse_mock.return_value | ||
|
|
||
| app.main() | ||
|
|
||
| parse_mock.assert_called_once_with() | ||
| generate_mock.assert_called_once_with( | ||
| args_mock.path, | ||
| prefix=args_mock.prefix, output="vds", files=args_mock.files, | ||
| source=None, | ||
| source_node=args_mock.source_node, | ||
| stripe_spacing=args_mock.stripe_spacing, | ||
| target_node=args_mock.target_node, | ||
| module_spacing=args_mock.module_spacing) |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,95 @@ | ||
| import sys | ||
| from argparse import ArgumentParser | ||
|
|
||
| from vdsgen import VDSGenerator | ||
|
|
||
|
|
||
| def parse_args(): | ||
| """Parse command line arguments.""" | ||
| parser = ArgumentParser() | ||
| parser.add_argument("path", type=str, | ||
| help="Root folder to create VDS in. Also where source " | ||
| "files are searched for if --prefix given.") | ||
|
|
||
| # Definition of file names in <path> - Common prefix or explicit list | ||
| file_definition = parser.add_mutually_exclusive_group(required=True) | ||
| file_definition.add_argument( | ||
| "-p", "--prefix", type=str, default=None, dest="prefix", | ||
| help="Prefix of files - e.g 'stripe_' to combine the images " | ||
| "'stripe_1.hdf5', 'stripe_2.hdf5' and 'stripe_3.hdf5' located " | ||
| "at <path>.") | ||
| file_definition.add_argument( | ||
| "-f", "--files", nargs="*", type=str, default=None, dest="files", | ||
| help="Manually define files to combine.") | ||
| parser.add_argument( | ||
| "-o", "--output", type=str, default=None, dest="output", | ||
| help="Output file name. Default is input file prefix with vds suffix.") | ||
|
|
||
| # Arguments required to allow VDS to be created before raw files exist | ||
| parser.add_argument( | ||
| "-e", "--empty", action="store_true", dest="empty", | ||
| help="Make empty VDS pointing to datasets that don't exist, yet.") | ||
| source_metadata = parser.add_argument_group() | ||
| source_metadata.add_argument( | ||
| "--frames", type=int, default=1, dest="frames", | ||
| help="Number of frames to combine into VDS.") | ||
| source_metadata.add_argument( | ||
| "--height", type=int, default=256, dest="height", | ||
| help="Height of raw datasets.") | ||
| source_metadata.add_argument( | ||
| "--width", type=int, default=1024, dest="width", | ||
| help="Width of raw datasets.") | ||
| source_metadata.add_argument( | ||
| "--data_type", type=str, default="uint16", dest="data_type", | ||
| help="Data type of raw datasets.") | ||
|
|
||
| # Arguments to override defaults | ||
| parser.add_argument("-s", "--stripe_spacing", nargs="?", type=int, | ||
| default=None, dest="stripe_spacing", | ||
| help="Spacing between two stripes in a module.") | ||
| parser.add_argument("-m", "--module_spacing", nargs="?", type=int, | ||
| default=None, dest="module_spacing", | ||
| help="Spacing between two modules.") | ||
| parser.add_argument("--source_node", nargs="?", type=str, default=None, | ||
| dest="source_node", | ||
| help="Data node in source HDF5 files.") | ||
| parser.add_argument("--target_node", nargs="?", type=str, default=None, | ||
| dest="target_node", | ||
| help="Data node in VDS file.") | ||
|
|
||
| args = parser.parse_args() | ||
|
|
||
| if args.empty and args.files is None: | ||
| parser.error( | ||
| "To make an empty VDS you must explicitly define --files for the " | ||
| "eventual raw datasets.") | ||
| if args.files is not None and len(args.files) < 2: | ||
| parser.error("Must define at least two files to combine.") | ||
|
|
||
| return args | ||
|
|
||
|
|
||
| def main(): | ||
| """Run program.""" | ||
| args = parse_args() | ||
|
|
||
| if args.empty: | ||
| source_metadata = dict(frames=args.frames, height=args.height, | ||
| width=args.width, dtype=args.data_type) | ||
| else: | ||
| source_metadata = None | ||
|
|
||
| gen = VDSGenerator(args.path, | ||
| prefix=args.prefix, files=args.files, | ||
| output=args.output, | ||
| source=source_metadata, | ||
| source_node=args.source_node, | ||
| target_node=args.target_node, | ||
| stripe_spacing=args.stripe_spacing, | ||
| module_spacing=args.module_spacing) | ||
|
|
||
| gen.generate_vds() | ||
|
|
||
|
|
||
| if __name__ == "__main__": | ||
| sys.exit(main()) |
Oops, something went wrong.