file-tag-parser 0.2.3__tar.gz

file_tag_parser-0.2.3/LICENSE

@@ -0,0 +1,201 @@
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file_tag_parser-0.2.3/PKG-INFO

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+Metadata-Version: 2.4
+Name: file-tag-parser
+Version: 0.2.3
+Summary: A tag-based filename parser for imaging data.
+Author-email: Rob F Cooper <robert.cooper@marquette.edu>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/OCVL/file-tag-parser
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=2.0
+Requires-Dist: parse>=1.2.0
+Requires-Dist: parse-type>=0.6.4
+Dynamic: license-file
+
+# file-tag-parser
+A tag-based filename parser for imaging data.
+
+This library is designed to make parsing of arbitrary filenames attainable and searchable via a pandas-based database. 
+Each filename can then be interpreted and/or manipulated for whatever processing and analysis is desired.
+
+At the moment, the library is solely dedicated to the interpretation of complex filenames using
+a "tagging system", to streamline their grouping and loading. This will likely be expanded in the future as needed.

file_tag_parser-0.2.3/README.md

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+# file-tag-parser
+A tag-based filename parser for imaging data.
+
+This library is designed to make parsing of arbitrary filenames attainable and searchable via a pandas-based database. 
+Each filename can then be interpreted and/or manipulated for whatever processing and analysis is desired.
+
+At the moment, the library is solely dedicated to the interpretation of complex filenames using
+a "tagging system", to streamline their grouping and loading. This will likely be expanded in the future as needed.

file_tag_parser-0.2.3/pyproject.toml

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+[build-system]
+requires = ["setuptools >= 77.0.3"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "file-tag-parser"
+version = "0.2.3"
+readme = "README.md"
+description = "A tag-based filename parser for imaging data."
+authors = [
+  { name="Rob F Cooper", email="robert.cooper@marquette.edu" },
+]
+license = "Apache-2.0"
+license-files = ["LICENSE"]
+requires-python = ">=3.9"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Operating System :: OS Independent",
+]
+dependencies = [
+    "pandas>=2.0",
+    "parse>=1.2.0",
+    "parse-type>=0.6.4"
+]
+
+[project.urls]
+Homepage = "https://github.com/OCVL/file-tag-parser"

file_tag_parser-0.2.3/setup.cfg

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+[egg_info]
+tag_build = 
+tag_date = 0
+

file_tag_parser-0.2.3/src/file_tag_parser.egg-info/PKG-INFO

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+Metadata-Version: 2.4
+Name: file-tag-parser
+Version: 0.2.3
+Summary: A tag-based filename parser for imaging data.
+Author-email: Rob F Cooper <robert.cooper@marquette.edu>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/OCVL/file-tag-parser
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pandas>=2.0
+Requires-Dist: parse>=1.2.0
+Requires-Dist: parse-type>=0.6.4
+Dynamic: license-file
+
+# file-tag-parser
+A tag-based filename parser for imaging data.
+
+This library is designed to make parsing of arbitrary filenames attainable and searchable via a pandas-based database. 
+Each filename can then be interpreted and/or manipulated for whatever processing and analysis is desired.
+
+At the moment, the library is solely dedicated to the interpretation of complex filenames using
+a "tagging system", to streamline their grouping and loading. This will likely be expanded in the future as needed.

file_tag_parser-0.2.3/src/file_tag_parser.egg-info/SOURCES.txt

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+LICENSE
+README.md
+pyproject.toml
+src/file_tag_parser.egg-info/PKG-INFO
+src/file_tag_parser.egg-info/SOURCES.txt
+src/file_tag_parser.egg-info/dependency_links.txt
+src/file_tag_parser.egg-info/requires.txt
+src/file_tag_parser.egg-info/top_level.txt
+src/ocvl/__init__.py
+src/ocvl/io/__init__.py
+src/ocvl/tags/__init__.py
+src/ocvl/tags/file_tag_parser.py
+src/ocvl/tags/json_format_constants.py
+tests/test_file_tag_parser.py

file_tag_parser-0.2.3/src/file_tag_parser.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

file_tag_parser-0.2.3/src/file_tag_parser.egg-info/requires.txt

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+pandas>=2.0
+parse>=1.2.0
+parse-type>=0.6.4

file_tag_parser-0.2.3/src/file_tag_parser.egg-info/top_level.txt

@@ -0,0 +1 @@
+ocvl

file_tag_parser-0.2.3/src/ocvl/__init__.py

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+try:
+    __import__('pkg_resources').declare_namespace(__name__)
+except ImportError:
+    import pkgutil
+    pkgutil.extend_path(__path__, __name__)

file_tag_parser-0.2.3/src/ocvl/io/__init__.py

@@ -0,0 +1,5 @@
+try:
+    __import__('pkg_resources').declare_namespace(__name__)
+except ImportError:
+    import pkgutil
+    pkgutil.extend_path(__path__, __name__)

file_tag_parser-0.2.3/src/ocvl/tags/__init__.py

@@ -0,0 +1,5 @@
+try:
+    __import__('pkg_resources').declare_namespace(__name__)
+except ImportError:
+    import pkgutil
+    pkgutil.extend_path(__path__, __name__)

file_tag_parser-0.2.3/src/ocvl/tags/file_tag_parser.py

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+import json
+from pathlib import Path
+
+import pandas as pd
+import parse
+from parse_type import TypeBuilder
+
+from ocvl.tags.json_format_constants import DataTags, DataFormat, AcquisiTags, MetaTags
+
+
+class FileTagParser():
+
+    json_dict = dict()
+    format_parsers = dict()
+
+    def __init__(self, format_dict=None):
+        # An optional parser for strings.
+        self.optional_parse = TypeBuilder.with_optional(lambda opt_str: str(opt_str))
+
+        for dataformat, form in format_dict.items():
+            self.format_parsers[dataformat] = parse.compile(form, {"s?":self.optional_parse})
+
+
+    @classmethod
+    def from_json(cls, json_file, root_group=None):
+        with open(json_file, 'r') as config_json_path:
+            json_dict = json.load(config_json_path)
+
+            return cls.from_dataformat_dict(json_dict, json_file, root_group=root_group)
+
+    @classmethod
+    def from_dataformat_dict(cls, json_dict_base=None, parse_path=None, root_group=None):
+
+        allFilesColumns = [AcquisiTags.DATASET, AcquisiTags.DATA_PATH, DataFormat.FORMAT_TYPE]
+        allFilesColumns.extend([d.value for d in DataTags])
+
+        cls.json_dict = json_dict_base
+
+        if root_group is not None:
+            sub_dict = json_dict_base.get(root_group)
+        else:
+            sub_dict = json_dict_base
+
+        cls.parser_extensions = ()
+
+        if sub_dict is not None and parse_path is not None:
+            form_dict = dict()
+
+            for format in DataFormat:
+                form = sub_dict.get(format)
+
+                if form is not None and isinstance(form, str):
+                    form_dict[format] = form
+
+                    cls.parser_extensions = cls.parser_extensions + (form[form.rfind(".", -5, -1):],) if form and form[form.rfind(".", -5,
+                                                                                                          -1):] not in cls.parser_extensions else cls.parser_extensions
+
+            metadata_form = None
+            metadata_params = None
+            if sub_dict.get(MetaTags.METATAG) is not None:
+                metadata_params = sub_dict.get(MetaTags.METATAG)
+                metadata_form = metadata_params.get(DataFormat.METADATA)
+
+            cls.parser_extensions = cls.parser_extensions + (metadata_form[metadata_form.rfind(".", -5, -1):],) if metadata_form and metadata_form[ metadata_form.rfind(".", -5, -1):] not in cls.parser_extensions else cls.parser_extensions
+
+            # Construct the parser we'll use for each of these forms
+            return cls(form_dict)
+        else:
+            return None
+
+    def parse_filename(self, file_string):
+
+        filename_tags = dict()
+        parsed_str = None
+        parser_used = None
+
+        for dataformat, parser in self.format_parsers.items():
+            parsed_str = parser.parse(file_string)
+
+            if parsed_str is not None:
+                parser_used = dataformat
+                break
+
+        if parsed_str is None:
+            return None, filename_tags
+
+        for formatstr in DataTags:
+            if formatstr in parsed_str.named:
+                if parsed_str[formatstr] is not None:
+                    filename_tags[formatstr.value] = parsed_str[formatstr]
+                else:
+                    filename_tags[formatstr.value] = ""
+
+        return parser_used, filename_tags
+
+    def parse_path(self, parse_path, recurse_me=False):
+        # Parse out the locations and filenames, store them in a hash table by location.
+        searchpath = Path(parse_path)
+        allFiles = list()
+        
+        if recurse_me:
+            for ext in self.parser_extensions:
+                for path in searchpath.rglob("*" + ext):
+                    format_type, file_info = self.parse_filename(path.name)
+                    if format_type is not None:
+                        file_info[DataFormat.FORMAT_TYPE] = format_type
+                        file_info[AcquisiTags.DATA_PATH] = path
+                        file_info[AcquisiTags.BASE_PATH] = path.parent
+                        file_info[AcquisiTags.DATASET] = None
+                        entry = pd.DataFrame.from_dict([file_info])
+
+                        allFiles.append(entry)
+        else:
+            for ext in self.parser_extensions:
+                for path in searchpath.glob("*" + ext):
+                    format_type, file_info = self.parse_filename(path.name)
+                    if format_type is not None:
+                        file_info[DataFormat.FORMAT_TYPE] = format_type
+                        file_info[AcquisiTags.DATA_PATH] = path
+                        file_info[AcquisiTags.BASE_PATH] = path.parent
+                        file_info[AcquisiTags.DATASET] = None
+                        entry = pd.DataFrame.from_dict([file_info])
+
+                        allFiles.append(entry)
+
+        if allFiles:
+            return pd.concat(allFiles, ignore_index=True)
+        else:
+            return pd.DataFrame()
+
+    def get_dict(self):
+        return self.json_dict

file_tag_parser-0.2.3/src/ocvl/tags/json_format_constants.py

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+from enum import StrEnum
+
+class DataFormat(StrEnum):
+    FORMAT_TYPE = "Data_Type"
+    IMAGE = "image_format"
+    VIDEO = "video_format"
+    MASK = "mask_format"
+    METADATA = "metadata_format"
+    QUERYLOC = "queryloc_format"
+
+# Will probably want to make a list of these corresponding to the version of the json files.
+# This verson assumes that we don't have any naming collisions; e.g. these constants aren't used in the filenames.
+class DataTags(StrEnum):
+    DATA_ID = "IDnum"
+    VIDEO_ID = "VidNum"
+    YEAR = "Year" # YYYY
+    MONTH = "Month" # MM
+    DAY = "Day" # DD
+    HOUR = "Hour"
+    MINUTE = "Minute"
+    SECOND = "Second"
+    EYE = "Eye"
+    RET_LOC_X = "LocX"
+    RET_LOC_Y = "LocY"
+    RET_LOC_Z = "LocZ"
+    FOV_WIDTH = "FOV_Width"
+    FOV_HEIGHT = "FOV_Height"
+    FOV_DEPTH = "FOV_Depth"
+    MODALITY = "Modality"
+    QUERYLOC = "QueryLoc"
+
+class MetaTags(StrEnum):
+    METATAG = "metadata"
+
+class AcquisiTags(StrEnum):
+    DATASET = "Dataset"
+    DATA_PATH = "Data_Path"
+    OUTPUT_PATH = "Output_Path"
+    VIDEO_PATH = "Video_Path"
+    IMAGE_PATH = "Image_Path"
+    QUERYLOC_PATH = "QueryLocation_Path"
+    BASE_PATH = "Base_Path"
+    MASK_PATH = "Mask_Path"
+    META_PATH = "Metadata_Path"
+
+

file_tag_parser-0.2.3/tests/test_file_tag_parser.py

@@ -0,0 +1,57 @@
+import os
+import unittest
+from pathlib import Path
+
+from ocvl.tags.file_tag_parser import FileTagParser
+from ocvl.tags.json_format_constants import DataFormat
+
+
+class FileTagTestCase(unittest.TestCase):
+    def setUp(self):
+        self.test_json_fname = Path(os.path.dirname(__file__)).joinpath("json_ex/test_json.json")
+
+        self.test_preanalysis_nomatch_vid = "00-36828_20230324_OD_(4,0)_1x1_6385_760nm1_extract_reg_cropped_piped.avi"
+        self.test_preanalysis_match_vid = "00-36828_20230324_OD_(4,0)_1x1_6385_760nm1_vid.avi"
+        self.test_preanalysis_nomatch_mask = "00-36828_20230324_OD_(4,0)_1x1_6385_760nm1_piped.avi"
+        self.test_preanalysis_match_mask = "00-36828_20230324_OD_(4,0)_1x1_6385_760nm1_mask.avi"
+
+
+    def test_json_parser_init(self):
+        parse_me = FileTagParser.from_json(self.test_json_fname)
+
+        self.assertEqual(len(parse_me.format_parsers), 0, "Parser should be empty, since we aren't supplying a base json group.")
+
+        parse_me = FileTagParser.from_json(self.test_json_fname, root_group="preanalysis")
+        self.assertGreater(len(parse_me.format_parsers), 0,"Parser have more than 0 parsers available, since we are supplying a base json group.")
+
+        self.assertNotEqual(len(parse_me.json_dict), 0, "JSON should not be empty.")
+
+
+    def test_json_file_parsing(self):
+
+        parse_me = FileTagParser.from_json(self.test_json_fname, root_group="preanalysis")
+        self.assertGreater(len(parse_me.format_parsers), 0,"Parser have more than 0 parsers available, since we are supplying a base json group.")
+
+        used_parser, file_tags = parse_me.parse_filename(self.test_preanalysis_nomatch_vid)
+        self.assertIsNone(used_parser, f"This filename ({self.test_preanalysis_nomatch_vid}) should not match any parsers in this object.")
+        self.assertEqual(len(file_tags), 0, f"This filename ({self.test_preanalysis_nomatch_vid}) should not produce any matches with the parser")
+
+        used_parser, file_tags = parse_me.parse_filename(self.test_preanalysis_match_vid)
+        self.assertEqual(used_parser, DataFormat.VIDEO,f"This filename ({self.test_preanalysis_match_vid}) match the video format parser.")
+        self.assertEqual(len(file_tags), 11, f"This filename ({self.test_preanalysis_match_vid}) should produce 11 matches with the parser.")
+        print(f"SUCCESS: Used parser: {used_parser}")
+        print(f"Found tags: {file_tags}")
+
+        used_parser, file_tags = parse_me.parse_filename(self.test_preanalysis_nomatch_mask)
+        self.assertIsNone(used_parser, f"This filename ({self.test_preanalysis_nomatch_mask}) should not match any parsers in this object.")
+        self.assertEqual(len(file_tags), 0, f"This filename ({self.test_preanalysis_nomatch_mask}) should not produce any matches with the parser")
+
+        used_parser, file_tags = parse_me.parse_filename(self.test_preanalysis_match_mask)
+        self.assertEqual(used_parser, DataFormat.MASK,f"This filename ({self.test_preanalysis_match_mask}) should match the mask format parser.")
+        self.assertEqual(len(file_tags), 11, f"This filename ({self.test_preanalysis_match_mask}) produce 11 matches with the parser.")
+        print(f"SUCCESS: Used parser: {used_parser}")
+        print(f"Found tags: {file_tags}")
+
+
+if __name__ == '__main__':
+    unittest.main()