pylinting, mypy, removal of unnecessary imports

FAIRmat-NFDI · Dec 7, 2023 · ff5cfa0 · ff5cfa0
1 parent 2090418
commit ff5cfa0
Show file tree

Hide file tree

Showing 14 changed files with 85 additions and 198 deletions.
diff --git a/pynxtools/dataconverter/readers/em/reader.py b/pynxtools/dataconverter/readers/em/reader.py
@@ -25,33 +25,27 @@
 
 from pynxtools.dataconverter.readers.em.concepts.nexus_concepts import NxEmAppDef
 
-from pynxtools.dataconverter.readers.em.subparsers.nxs_mtex import NxEmNxsMTexSubParser
+# from pynxtools.dataconverter.readers.em.subparsers.nxs_mtex import NxEmNxsMTexSubParser
 
 from pynxtools.dataconverter.readers.em.subparsers.nxs_pyxem import NxEmNxsPyxemSubParser
 
 from pynxtools.dataconverter.readers.em.utils.default_plots import NxEmDefaultPlotResolver
 
-from pynxtools.dataconverter.readers.em.geometry.convention_mapper \
-    import NxEmConventionMapper
+# from pynxtools.dataconverter.readers.em.geometry.convention_mapper import NxEmConventionMapper
 
-"""
-from pynxtools.dataconverter.readers.em_om.utils.generic_eln_io \
-    import NxEmOmGenericElnSchemaParser
-
-from pynxtools.dataconverter.readers.em_om.utils.orix_ebsd_parser \
-    import NxEmOmOrixEbsdParser
-
-from pynxtools.dataconverter.readers.em_om.utils.mtex_ebsd_parser \
-    import NxEmOmMtexEbsdParser
-
-from pynxtools.dataconverter.readers.em_om.utils.zip_ebsd_parser \
-    import NxEmOmZipEbsdParser
-
-from pynxtools.dataconverter.readers.em_om.utils.dream3d_ebsd_parser \
-    import NxEmOmDreamThreedEbsdParser
-
-from pynxtools.dataconverter.readers.em_om.utils.em_nexus_plots \
-    import em_om_default_plot_generator"""
+# remaining subparsers to be implemented and merged into this one
+# from pynxtools.dataconverter.readers.em_om.utils.generic_eln_io \
+#     import NxEmOmGenericElnSchemaParser
+# from pynxtools.dataconverter.readers.em_om.utils.orix_ebsd_parser \
+#     import NxEmOmOrixEbsdParser
+# from pynxtools.dataconverter.readers.em_om.utils.mtex_ebsd_parser \
+#     import NxEmOmMtexEbsdParser
+# from pynxtools.dataconverter.readers.em_om.utils.zip_ebsd_parser \
+#     import NxEmOmZipEbsdParser
+# from pynxtools.dataconverter.readers.em_om.utils.dream3d_ebsd_parser \
+#     import NxEmOmDreamThreedEbsdParser
+# from pynxtools.dataconverter.readers.em_om.utils.em_nexus_plots \
+#     import em_om_default_plot_generator
 
 
 class EmReader(BaseReader):
@@ -127,7 +121,7 @@ def read(self,
 
         # add further with resolving cases
         # if file_path is an HDF5 will use hfive parser
-        sub_parser = "nxs_pyxem"
+        # sub_parser = "nxs_pyxem"
         subparser = NxEmNxsPyxemSubParser(entry_id, file_paths[0])
         subparser.parse(template)
         # exit(1)

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_apex.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_apex.py
@@ -19,19 +19,9 @@
 
 import numpy as np
 import h5py
-from itertools import groupby
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
+from typing import Dict
 from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation, Orientation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
+from orix.quaternion import Orientation
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import \
@@ -48,8 +38,8 @@ def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
         self.tmp = {}
-        self.supported_version = {}
-        self.version = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_base.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_base.py
@@ -17,17 +17,9 @@
 #
 """(Sub-)parser mapping concepts and content from EDAX/AMETEK *.edaxh5 (APEX) files on NXem."""
 
-import os
-import glob
-import re
-import sys
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-import yaml
-import json
-# import imageio.v3 as iio
-from PIL import Image as pil
+from typing import Dict, List
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_concept import \
     IS_GROUP, IS_REGULAR_DATASET, IS_COMPOUND_DATASET, IS_ATTRIBUTE, \
@@ -64,24 +56,24 @@ def __init__(self, file_path: str = ""):
         #   an instance of a file whose schema belongs to the H5OINA family of HDF5 container formats
         #   specifically using version 5
         self.prfx = None
-        self.tmp = {}
+        self.tmp: Dict = {}
         self.source = None
         self.file_path = None
         # collection of instance path
-        self.groups = {}
-        self.datasets = {}
-        self.attributes = {}
-        self.instances = {}
+        self.groups: Dict = {}
+        self.datasets: Dict = {}
+        self.attributes: Dict = {}
+        self.instances: Dict = {}
         # collection of template
-        self.template_groups = []
-        self.template_datasets = []
-        self.template_attributes = []
-        self.templates = {}
+        self.template_groups: List = []
+        self.template_datasets: List = []
+        self.template_attributes: List = []
+        self.templates: Dict = {}
         self.h5r = None
         if file_path is not None and file_path != "":
             self.file_path = file_path
         else:
-            raise ValueError(f"{__class__.__name__} needs proper instantiation !")
+            raise ValueError(f"{__name__} needs proper instantiation !")
 
     def init_named_cache(self, ckey: str):
         """Init a new cache for normalized EBSD data if not existent."""

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_bruker.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_bruker.py
@@ -17,29 +17,16 @@
 #
 """(Sub-)parser mapping concepts and content from Bruker *.h5 files on NXem."""
 
-import os
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-from itertools import groupby
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
+from typing import Dict
 from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import \
     EBSD_MAP_SPACEGROUP, read_strings_from_dataset, all_equal, format_euler_parameterization
 from pynxtools.dataconverter.readers.em.examples.ebsd_database import \
-    ASSUME_PHASE_NAME_TO_SPACE_GROUP, HEXAGONAL_GRID, SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN
+    ASSUME_PHASE_NAME_TO_SPACE_GROUP, SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN  # HEXAGONAL_GRID
 from pynxtools.dataconverter.readers.em.utils.get_scan_points import \
     get_scan_point_coords
 
@@ -49,9 +36,9 @@ class HdfFiveBrukerEspritReader(HdfFiveBaseParser):
     def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
-        self.tmp = {}
-        self.supported_version = {}
-        self.version = {}
+        self.tmp: Dict = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_concept.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_concept.py
@@ -17,14 +17,16 @@
 #
 """Constants and utilities used when parsing concepts from HDF5 files."""
 
+from typing import Dict
+
 IS_GROUP = 0
 IS_REGULAR_DATASET = 1
 IS_COMPOUND_DATASET = 2
 IS_FIELD_IN_COMPOUND_DATASET = 3
 IS_ATTRIBUTE = 4
-VERSION_MANAGEMENT = {"tech_partner": [],
-                      "schema_name": [], "schema_version": [],
-                      "writer_name": [], "writer_version": []}
+VERSION_MANAGEMENT: Dict = {"tech_partner": [],
+                            "schema_name": [], "schema_version": [],
+                            "writer_name": [], "writer_version": []}
 
 
 class Concept():

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_dreamthreed.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_dreamthreed.py
@@ -17,28 +17,15 @@
 #
 """(Sub-)parser mapping concepts and content from community *.dream3d files on NXem."""
 
-import os
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
-from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
+from typing import Dict
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import \
-    EBSD_MAP_SPACEGROUP, read_strings_from_dataset, all_equal, format_euler_parameterization
+    read_strings_from_dataset  # EBSD_MAP_SPACEGROUP
 from pynxtools.dataconverter.readers.em.examples.ebsd_database import \
-    ASSUME_PHASE_NAME_TO_SPACE_GROUP, HEXAGONAL_GRID, SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN
+    SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN  # ASSUME_PHASE_NAME_TO_SPACE_GROUP, HEXAGONAL_GRID
 
 # DREAM3D implements essentially a data analysis workflow with individual steps
 # in the DREAM3D jargon each step is referred to as a filter, filters have well-defined
@@ -97,9 +84,9 @@ def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
         self.tmp = {}
-        self.path_registry = {}
-        self.supported_version = {}
-        self.version = {}
+        self.path_registry: Dict = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_ebsd.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_ebsd.py
@@ -17,28 +17,16 @@
 #
 """(Sub-)parser mapping concepts and content from community *.h5/*.h5ebsd files on NXem."""
 
-import os
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
+from typing import Dict
 from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import \
     EBSD_MAP_SPACEGROUP, read_strings_from_dataset, all_equal, format_euler_parameterization
 from pynxtools.dataconverter.readers.em.examples.ebsd_database import \
-    ASSUME_PHASE_NAME_TO_SPACE_GROUP, HEXAGONAL_GRID, SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN
+    ASSUME_PHASE_NAME_TO_SPACE_GROUP, SQUARE_GRID, REGULAR_TILING, FLIGHT_PLAN  # HEXAGONAL_GRID
 from pynxtools.dataconverter.readers.em.utils.get_scan_points import \
     get_scan_point_coords
 
@@ -49,8 +37,8 @@ def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
         self.tmp = {}
-        self.supported_version = {}
-        self.version = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_edax.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_edax.py
@@ -17,23 +17,10 @@
 #
 """(Sub-)parser mapping concepts and content from EDAX/AMETEK *.oh5/*.h5 (OIM Analysis) files on NXem."""
 
-import os
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-from itertools import groupby
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
+from typing import Dict
 from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import EULER_SPACE_SYMMETRY, \
@@ -48,8 +35,8 @@ def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
         self.tmp = {}
-        self.supported_version = {}
-        self.version = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()

diff --git a/pynxtools/dataconverter/readers/em/subparsers/hfive_emsoft.py b/pynxtools/dataconverter/readers/em/subparsers/hfive_emsoft.py
@@ -17,23 +17,9 @@
 #
 """(Sub-)parser mapping concepts and content from Marc deGraeff's EMsoft *.h5 files on NXem."""
 
-import os
-from typing import Dict, Any, List
 import numpy as np
 import h5py
-from itertools import groupby
-# import imageio.v3 as iio
-from PIL import Image as pil
-
-import diffsims
-import orix
-from diffpy.structure import Lattice, Structure
-from orix import plot
-from orix.crystal_map import create_coordinate_arrays, CrystalMap, PhaseList
-from orix.quaternion import Rotation
-from orix.vector import Vector3d
-
-import matplotlib.pyplot as plt
+from typing import Dict
 
 from pynxtools.dataconverter.readers.em.subparsers.hfive_base import HdfFiveBaseParser
 from pynxtools.dataconverter.readers.em.utils.hfive_utils import read_strings_from_dataset
@@ -45,8 +31,8 @@ def __init__(self, file_path: str = ""):
         super().__init__(file_path)
         self.prfx = None
         self.tmp = {}
-        self.supported_version = {}
-        self.version = {}
+        self.supported_version: Dict = {}
+        self.version: Dict = {}
         self.init_support()
         self.supported = False
         self.check_if_supported()