Equalized all call lines for individual parsers, removed deprecated t…

…erm subparser

src/pynxtools_em/parsers/image_png_protochips.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for exemplar reading of raw PNG files collected on a TEM with Protochip heating_chip."""
+"""Parser for exemplar reading of raw PNG files collected on a TEM with Protochip heating_chip."""
 
 import datetime
 import mmap

src/pynxtools_em/parsers/image_tiff_hitachi.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing Hitachi-specific content in TIFF files."""
+"""Parser for harmonizing Hitachi-specific content in TIFF files."""
 
 import mmap
 from tokenize import TokenError
@@ -199,7 +199,5 @@ def process_event_data_em_metadata(self, template: dict) -> dict:
         # we assume for now dynamic quantities can just be repeated
         identifier = [self.entry_id, self.event_id, 1]
         for cfg in [HITACHI_VARIOUS_DYNAMIC_TO_NX_EM, HITACHI_VARIOUS_STATIC_TO_NX_EM]:
-            add_specific_metadata_pint(
-                cfg, self.flat_dict_meta, identifier, template
-            )
+            add_specific_metadata_pint(cfg, self.flat_dict_meta, identifier, template)
         return template

src/pynxtools_em/parsers/image_tiff_jeol.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing JEOL specific content in TIFF files."""
+"""Parser for harmonizing JEOL specific content in TIFF files."""
 
 import mmap
 from typing import Dict, List
@@ -111,8 +111,7 @@ def check_if_tiff_jeol(self):
                     print(f"{key}______{type(value)}____{value}")
 
             if all(
-                key in self.flat_dict_meta
-                for key in ["SEM_DATA_VERSION", "CM_LABEL"]
+                key in self.flat_dict_meta for key in ["SEM_DATA_VERSION", "CM_LABEL"]
             ):
                 if (self.flat_dict_meta["SEM_DATA_VERSION"] == 1) and (
                     self.flat_dict_meta["CM_LABEL"] == "JEOL"
@@ -178,9 +177,7 @@ def process_event_data_em_data(self, template: dict) -> dict:
                     # JEOL-specific conversion for micron bar pixel to physical length
                     resolution = int(self.flat_dict_meta["SM_MICRON_BAR"])
                     physical_length = (
-                        self.flat_dict_meta["SM_MICRON_MARKER"]
-                        .to(ureg.meter)
-                        .magnitude
+                        self.flat_dict_meta["SM_MICRON_MARKER"].to(ureg.meter).magnitude
                     )
                     # resolution many pixel represent physical_length scanned surface
                     # assuming square pixel

src/pynxtools_em/parsers/image_tiff_point_electronic.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing point electronic DISS specific content in TIFF files."""
+"""Parser for harmonizing point electronic DISS specific content in TIFF files."""
 
 import mmap
 from typing import Dict
@@ -38,9 +38,13 @@ def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False
         self.event_id = 1
         self.verbose = verbose
         self.tmp: Dict = {"data": None, "flat_dict_meta": fd.FlatDict({})}
-        self.version: Dict = {"trg": {"tech_partner": ["point electronic"],
-                                      "schema_name": ["DISS"],
-                                      "schema_version": ["5.15.31.0"]}}
+        self.version: Dict = {
+            "trg": {
+                "tech_partner": ["point electronic"],
+                "schema_name": ["DISS"],
+                "schema_version": ["5.15.31.0"],
+            }
+        }
         self.supported = False
         self.check_if_tiff_point_electronic()
 

src/pynxtools_em/parsers/image_tiff_tescan.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing TESCAN-specific content in TIFF files."""
+"""Parser for harmonizing TESCAN-specific content in TIFF files."""
 
 import mmap
 from typing import Dict, List

src/pynxtools_em/parsers/image_tiff_tfs.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing ThermoFisher-specific content in TIFF files."""
+"""Parser for harmonizing ThermoFisher-specific content in TIFF files."""
 
 import mmap
 from typing import Dict
@@ -24,6 +24,7 @@
 import numpy as np
 from PIL import Image
 from PIL.TiffTags import TAGS
+
 # https://www.loc.gov/preservation/digital/formats/content/tiff_tags.shtml
 from pynxtools_em.concepts.mapping_functors import add_specific_metadata
 from pynxtools_em.configurations.image_tiff_tfs_cfg import (
@@ -137,9 +138,13 @@ def get_metadata(self):
                             if value != "":
                                 # execution order of the check here matters!
                                 if value.isdigit() is True:
-                                    self.flat_dict_meta[f"{parent}/{term}"] = np.int64(value)
+                                    self.flat_dict_meta[f"{parent}/{term}"] = np.int64(
+                                        value
+                                    )
                                 elif if_str_represents_float(value) is True:
-                                    self.flat_dict_meta[f"{parent}/{term}"] = np.float64(value)
+                                    self.flat_dict_meta[f"{parent}/{term}"] = (
+                                        np.float64(value)
+                                    )
                                 else:
                                     self.flat_dict_meta[f"{parent}/{term}"] = value
                         else:

src/pynxtools_em/parsers/image_tiff_zeiss.py

@@ -15,7 +15,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 #
-"""Subparser for harmonizing Zeiss-specific content in TIFF files."""
+"""Parser for harmonizing Zeiss-specific content in TIFF files."""
 
 import mmap
 import re
@@ -46,9 +46,13 @@ def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False
         self.event_id = 1
         self.verbose = verbose
         self.flat_dict_meta = fd.FlatDict({}, "/")
-        self.version: Dict = {"trg": {"tech_partner": ["Zeiss"],
-                                      "schema_name": ["Zeiss"],
-                                      "schema_version": ["V06.03.00.00 : 15-Dec-17"]}}
+        self.version: Dict = {
+            "trg": {
+                "tech_partner": ["Zeiss"],
+                "schema_name": ["Zeiss"],
+                "schema_version": ["V06.03.00.00 : 15-Dec-17"],
+            }
+        }
         self.supported = False
         self.check_if_tiff_zeiss()
 
@@ -91,7 +95,7 @@ def get_metadata(self, payload: str):
                     elif len(tmp) == 2 and tmp[1] == "X":
                         self.flat_dict_meta[line] = ureg.Quantity(tmp[0])
                     elif len(tmp) == 3 and tmp[1] == "K" and tmp[2] == "X":
-                        self.flat_dict_meta[line] = (ureg.Quantity(tmp[0]) * 1000.0)
+                        self.flat_dict_meta[line] = ureg.Quantity(tmp[0]) * 1000.0
                     else:
                         try:
                             self.flat_dict_meta[line] = ureg.Quantity(token[1])
@@ -198,9 +202,7 @@ def process_event_data_em_data(self, template: dict) -> dict:
                 scan_unit = {"i": "m", "j": "m"}
                 if "APImagePixelSize" in self.flat_dict_meta:
                     pixel_size = (
-                        self.flat_dict_meta["APImagePixelSize"]
-                        .to(ureg.meter)
-                        .magnitude
+                        self.flat_dict_meta["APImagePixelSize"].to(ureg.meter).magnitude
                     )
                     sxy = {"i": pixel_size, "j": pixel_size}
                 else:

src/pynxtools_em/parsers/nxs_imgs.py

@@ -26,15 +26,15 @@
 class NxEmImagesParser:
     """Map content from different type of image files on an instance of NXem."""
 
-    def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
         """Overwrite constructor of the generic reader."""
+        self.file_path = file_path
         if entry_id > 0:
             self.entry_id = entry_id
         else:
             self.entry_id = 1
-        self.file_path = file_path
-        self.cache = {"is_filled": False}
         self.verbose = verbose
+        self.cache = {"is_filled": False}
 
     def identify_image_type(self):
         """Identify if image matches known mime type and has content for which parser exists."""

src/pynxtools_em/parsers/nxs_mtex.py

@@ -50,14 +50,14 @@ def hfive_to_template(payload):
 class NxEmNxsMTexParser:
     """Map content from *.nxs.mtex files on an instance of NXem."""
 
-    def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
+        self.file_path = file_path
         if entry_id > 0:
             self.entry_id = entry_id
         else:
             self.entry_id = 1
-        self.file_path = file_path
-        self.supported = False
         self.verbose = verbose
+        self.supported = False
         self.check_if_mtex_nxs()
 
     def check_if_mtex_nxs(self):

src/pynxtools_em/parsers/nxs_nion.py

@@ -58,21 +58,19 @@
 class NionProjectParser:
     """Parse (zip-compressed archive of a) nionswift project with its content."""
 
-    def __init__(
-        self, entry_id: int = 1, input_file_path: str = "", verbose: bool = True
-    ):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = True):
         """Class wrapping swift parser."""
-        if input_file_path is not None and input_file_path != "":
-            self.file_path = input_file_path
+        if file_path is not None and file_path != "":
+            self.file_path = file_path
         if entry_id > 0:
             self.entry_id = entry_id
         else:
             self.entry_id = 1
         self.event_id = 1
+        self.verbose = verbose
         # counters which keep track of how many instances of NXevent_data_em have
         # been instantiated, this implementation currently maps each display_items
         # onto an own NXevent_data_em instance
-        self.verbose = verbose
         self.file_path_sha256 = None
         self.tmp: Dict = {}
         self.proj_file_dict: Dict = {}

src/pynxtools_em/parsers/nxs_pyxem.py

@@ -106,13 +106,14 @@ def get_ipfdir_legend(ipf_key):
 class NxEmNxsPyxemParser:
     """Map content from different type of *.h5 files on an instance of NXem."""
 
-    def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
         """Overwrite constructor of the generic reader."""
+        self.file_path = file_path
         if entry_id > 0:
             self.entry_id = entry_id
         else:
             self.entry_id = 1
-        self.file_path = file_path
+        self.verbose = verbose
         self.id_mgn = {
             "event": 1,
             "event_img": 1,
@@ -121,7 +122,6 @@ def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False
             "eds_img": 1,
         }
         self.cache = {"is_filled": False}
-        self.verbose = verbose
 
     def parse(self, template: dict) -> dict:
         hfive_parser_type = self.identify_hfive_type()

src/pynxtools_em/parsers/rsciio_base.py

@@ -42,4 +42,3 @@ def __init__(self, file_path: str = ""):
         if file_path is not None and file_path != "":
             self.file_path = file_path
         self.tmp: Dict = {}
-        self.file_path_sha256 = None

src/pynxtools_em/parsers/rsciio_gatan.py

@@ -42,7 +42,7 @@
 class RsciioGatanParser(RsciioBaseParser):
     """Read Gatan Digital Micrograph dm3/dm4 formats."""
 
-    def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
         super().__init__(file_path)
         if entry_id > 0:
             self.entry_id = entry_id

src/pynxtools_em/parsers/rsciio_velox.py

@@ -54,25 +54,29 @@
 class RsciioVeloxParser(RsciioBaseParser):
     """Read Velox EMD File Format emd."""
 
-    def __init__(self, entry_id: int = 1, file_path: str = "", verbose: bool = False):
+    def __init__(self, file_path: str = "", entry_id: int = 1, verbose: bool = False):
         super().__init__(file_path)
         if entry_id > 0:
             self.entry_id = entry_id
         else:
             self.entry_id = 1
+        self.verbose = verbose
         self.id_mgn: Dict = {
             "event": 1,
             "event_img": 1,
             "event_spc": 1,
             "roi": 1,
             "eds_img": 1,
         }
-        self.verbose = verbose
-        self.tmp: Dict = {}
-        self.version: Dict = {"trg": {"Core/MetadataDefinitionVersion": ["7.9"],
-            "Core/MetadataSchemaVersion": ["v1/2013/07"]},
-            "src": {"Core/MetadataDefinitionVersion": None,
-            "Core/MetadataSchemaVersion": None}
+        self.version: Dict = {
+            "trg": {
+                "Core/MetadataDefinitionVersion": ["7.9"],
+                "Core/MetadataSchemaVersion": ["v1/2013/07"],
+            },
+            "src": {
+                "Core/MetadataDefinitionVersion": None,
+                "Core/MetadataSchemaVersion": None,
+            },
         }
         self.obj_idx_supported: List = []
         self.supported = False

src/pynxtools_em/reader.py

@@ -105,25 +105,25 @@ def read(
 
         print("Parse and map pieces of information within files from tech partners...")
         if len(case.dat) == 1:  # no sidecar file
-            images = NxEmImagesParser(entry_id, case.dat[0], verbose=False)
+            images = NxEmImagesParser(case.dat[0], entry_id, verbose=False)
             images.parse(template)
 
-            velox = RsciioVeloxParser(entry_id, case.dat[0], verbose=False)
+            velox = RsciioVeloxParser(case.dat[0], entry_id, verbose=False)
             velox.parse(template)
 
-            gatan = RsciioGatanParser(entry_id, case.dat[0], verbose=False)
+            gatan = RsciioGatanParser(case.dat[0], entry_id, verbose=False)
             gatan.parse(template)
 
-            nxs_mtex = NxEmNxsMTexParser(entry_id, case.dat[0], verbose=False)
+            nxs_mtex = NxEmNxsMTexParser(case.dat[0], entry_id, verbose=False)
             nxs_mtex.parse(template)
 
-            nxs_pyxem = NxEmNxsPyxemParser(entry_id, case.dat[0], verbose=False)
+            nxs_pyxem = NxEmNxsPyxemParser(case.dat[0], entry_id, verbose=False)
             nxs_pyxem.parse(template)
 
-            nxs_nion = NionProjectParser(entry_id, case.dat[0], verbose=False)
+            nxs_nion = NionProjectParser(case.dat[0], entry_id, verbose=False)
             nxs_nion.parse(template)
 
-            # zip_parser = NxEmOmZipEbsdParser(case.dat[0], entry_id)
+            # zip_parser = NxEmOmZipEbsdParser(case.dat[0], entry_id, verbose=False)
             # zip_parser.parse(template)
         if len(case.dat) >= 1:  # optional sidecar file
             tescan = TescanTiffParser(case.dat, entry_id)