micress-micpy 0.2.15b0__py3-none-any.whl → 0.2.17b0__py3-none-any.whl

micpy/bin.py

@@ -1,4 +1,4 @@
-"""This module provides methods to read and write binary files."""
+"""The `micpy.bin` module provides methods to read and write binary files."""
 
 from dataclasses import dataclass
 from typing import Callable, IO, List, Tuple, Generator
@@ -420,26 +420,27 @@ class Field(np.ndarray):
         vmin: float = None,
         vmax: float = None,
         cmap: str = "micpy",
-    ):
+    ) -> Tuple["matplotlib.Figure", "matplotlib.Axes"]:
         """Plot a slice of the field.
 
         Args:
-            plane (str, optional): Plane of the slice. Defaults to "xz".
-            slice_id (int, optional): Slice ID. Defaults to 0.
-            title (str, optional): Title of the plot. Defaults to None.
-            xlabel (str, optional): Label of the x-axis. Defaults to None (auto).
-            ylabel (str, optional): Label of the y-axis. Defaults to None (auto).
-            figsize (Tuple[float, float], optional): Figure size. Defaults to None (auto).
-            dpi (int, optional): Figure DPI. Defaults to None (auto).
-            aspect (str, optional): Aspect ratio. Defaults to "equal".
-            ax (Axes, optional): Axes to plot on. Defaults to None.
-            cax (Axes, optional): Axes to plot color bar on. Defaults to None.
-            vmin (float, optional): Minimum value of the color bar. Defaults to None.
-            vmax (float, optional): Maximum value of the color bar. Defaults to None.
-            cmap (str, optional): Color map. Defaults to "micpy".
+            plane (str, optional): Plane of the slice. Defaults to `xz`.
+            slice_id (int, optional): Slice ID. Defaults to `0`.
+            title (str, optional): Title of the plot. Defaults to `None`.
+            xlabel (str, optional): Label of the x-axis. Defaults to `None` (auto).
+            ylabel (str, optional): Label of the y-axis. Defaults to `None` (auto).
+            figsize (Tuple[float, float], optional): Figure size. Defaults to `None` 
+                (auto).
+            dpi (int, optional): Figure DPI. Defaults to `None` (auto).
+            aspect (str, optional): Aspect ratio. Defaults to `equal`.
+            ax (Axes, optional): Axes to plot on. Defaults to `None`.
+            cax (Axes, optional): Axes to plot color bar on. Defaults to `None`.
+            vmin (float, optional): Minimum value of the color bar. Defaults to `None`.
+            vmax (float, optional): Maximum value of the color bar. Defaults to `None`.
+            cmap (str, optional): Color map. Defaults to `micpy`.
 
         Returns:
-            Tuple[Figure, Axes]: Figure and axes of the plot.
+            Figure and axes of the plot.
         """
         if matplotlib is None:
             raise ImportError("matplotlib is not installed")
@@ -517,20 +518,21 @@ class FieldList(List[Field]):
         figsize: Tuple[float, float] = None,
         dpi: int = None,
         **kwargs,
-    ):
+    ) -> Tuple["matplotlib.Figure", "matplotlib.Axes"]:
         """Plot the fields in a grid.
 
         Args:
-            cols (int, optional): Number of columns. Defaults to None (auto).
-            normalize (bool, optional): Normalize the color bar. Defaults to False.
-            sharex (bool, optional): Share x-axis. Defaults to False.
-            sharey (bool, optional): Share y-axis. Defaults to False.
-            figsize (Tuple[float, float], optional): Figure size. Defaults to None (auto).
-            dpi (int, optional): Figure DPI. Defaults to None (auto).
-            **kwargs: Keyword arguments passed to Field.plot().
+            cols (int, optional): Number of columns. Defaults to `None` (auto).
+            normalize (bool, optional): Normalize the color bar. Defaults to `False`.
+            sharex (bool, optional): Share x-axis. Defaults to `False`.
+            sharey (bool, optional): Share y-axis. Defaults to `False`.
+            figsize (Tuple[float, float], optional): Figure size. Defaults to `None` 
+                (auto).
+            dpi (int, optional): Figure DPI. Defaults to `None` (auto).
+            **kwargs: Keyword arguments passed to `Field.plot()`.
 
         Returns:
-            Tuple[Figure, Axes]: Figure and axes of the plot.
+            Figure and axes of the plot.
         """
         if matplotlib is None:
             raise ImportError("matplotlib is not installed")
@@ -583,11 +585,12 @@ class File:
 
         Args:
             filename (str): File name.
-            chunk_size (int, optional): Chunk size in bytes. Defaults to 8388608 (8 MiB).
-            verbose (bool, optional): Verbose output. Defaults to True.
+            chunk_size (int, optional): Chunk size in bytes. Defaults to `8388608`
+                (8 MiB).
+            verbose (bool, optional): Verbose output. Defaults to `True`.
 
         Raises:
-            FileNotFoundError: If file is not found.
+            `FileNotFoundError`: If file is not found.
         """
         if not os.path.isfile(filename):
             raise FileNotFoundError(f"File not found: {filename}")
@@ -697,7 +700,7 @@ class File:
         """Get the times of the fields in the file.
 
         Returns:
-            List[float]: List of times.
+            List of times.
         """
         return [position.time for position in self.index()]
 
@@ -706,7 +709,7 @@ class File:
 
         Args:
             shape (Tuple[int, int, int]): Shape of the geometry.
-            spacing (Tuple[float, float, float]): Spacing of the geometry.
+            spacing (Tuple[float, float, float]): Spacing of the geometry in μm³.
         """
 
         self.shape = np.array(shape)
@@ -721,24 +724,28 @@ class File:
 
         Args:
             filename (str): Filename of a geometry file.
-            type (Type, optional): Data type to be read. Defaults to Type.EXTENDED.
-            compressed (bool, optional): True if file is compressed, False otherwise.
-                Defaults to True.
+            type (Type, optional): Data type to be read. Defaults to `Type.EXTENDED`.
+            compressed (bool, optional): `True` if file is compressed, `False` 
+                otherwise. Defaults to True.
         """
         geo_dict = geo.read(filename, type=type, compressed=compressed)
-        self.set_geo(geo_dict["shape"], geo_dict["spacing"])
+
+        shape = geo_dict["shape"]
+        spacing = utils.convert_si(geo_dict["spacing"], "cm", "μm")
+
+        self.set_geo(shape, spacing)
 
     def find_geo(self, type: geo.Type = geo.Type.EXTENDED, compressed: bool = None):
         """Find geometry file and read it.
 
         Args:
-            type (Type, optional): Data type to be read. Defaults to Type.EXTENDED.
+            type (Type, optional): Data type to be read. Defaults to `Type.EXTENDED`.
             compressed (bool, optional): True if file is compressed, False otherwise.
-                Defaults to None (auto).
+                Defaults to `None` (auto).
 
         Raises:
-            GeometryFileNotFoundError: If no geometry file is found.
-            MultipleGeometryFilesError: If multiple geometry files are found.
+            `GeometryFileNotFoundError`: If no geometry file is found.
+            `MultipleGeometryFilesError`: If multiple geometry files are found.
         """
         filename = geo.find(self._filename)
 
@@ -764,25 +771,25 @@ class File:
         self._info(f"Grid Shape (Cell Count): {tuple(cells)}")
         self._info(f"Grid Spacing (Cell Size): {tuple(spacing)}μm³")
 
-    def iterate(self):
+    def iterate(self) -> Generator[Field, None, None]:
         """Iterate over fields in the file.
 
         Returns:
-            Field: Field data.
+            Field data.
         """
         for position in self.index():
             yield Field.read(position, shape=self.shape, spacing=self.spacing)
 
-    def read(self, key: int or slice or list or Callable[[Field], bool] = None):
+    def read(self, key: int or slice or list or Callable[[Field], bool] = None) -> FieldList:
         """Read a field from the file.
 
         Args:
             key (int or list or slice or Callable[[Field], bool], optional): Field ID,
                 list of field IDs, a slice object, or a condition function.
-                Defaults to None.
+                Defaults to `None`.
 
         Returns:
-            FieldList: List of fields.
+            List of fields.
         """
 
         def read_field(self, field_id: int or slice or list):

micpy/geo.py

@@ -1,4 +1,4 @@
-"""This module provides methods to read and write geometry files."""
+"""The `micpy.geo` modules provides methods to read and write geometry files."""
 
 import enum
 import gzip
@@ -31,11 +31,11 @@ BASIC_MODEL = [
 
 EXTENSION_MODEL = [
     ("extension_header", np.int32),
-    ("version", np.string_, 10),
-    ("compile_date", np.string_, 10),
-    ("run_date", np.string_, 10),
-    ("platform", np.string_, 10),
-    ("precision", np.string_, 10),
+    ("version", np.bytes_, 10),
+    ("compile_date", np.bytes_, 10),
+    ("run_date", np.bytes_, 10),
+    ("platform", np.bytes_, 10),
+    ("precision", np.bytes_, 10),
     ("extension_footer", np.int32),
 ]
 
@@ -59,7 +59,7 @@ class MultipleGeometryFilesError(GeometryFileError):
     """Raised when multiple potential geometry files are found."""
 
 
-def find(filename: str) -> str:
+def find(filename: str) -> Path:
     """Find the geometry file for a given binary file.
 
     This method assumes that (a) both files share a common basename and (b) the
@@ -69,7 +69,7 @@ def find(filename: str) -> str:
         filename (str): Filename of a binary file.
 
     Returns:
-        Path: Path to the geometry file.
+        Path to the geometry file.
     """
     basename = _get_basename(Path(filename))
     matches = list(basename.parent.glob(f"{basename.name}[._]geoF*"))
@@ -91,10 +91,10 @@ def read(filename: str, type: Type = Type.EXTENDED, compressed: bool = True) ->
         filename (str): Filename of a geometry file.
         type (Type, optional): Data type to be read.
         compressed (bool, optional): True if file is compressed, False otherwise.
-            Defaults to True.
+            Defaults to `True`.
 
     Returns:
-        dict: Dictionary representation of the geometry file.
+        Dictionary representation of the geometry file.
     """
     array_data = read_ndarray(filename, type, compressed)
     return _ndarray_to_dict(array_data)
@@ -107,12 +107,12 @@ def read_ndarray(
 
     Args:
         filename (str): Filename of a geometry file.
-        type (Type, optional): Data type to be read. Defaults to Type.EXTENDED.
-        compressed (bool, optional): True if file is compressed, False otherwise.
-            Defaults to True.
+        type (Type, optional): Data type to be read. Defaults to `Type.EXTENDED`.
+        compressed (bool, optional): `True` if file is compressed, `False` otherwise.
+            Defaults to `True`.
 
     Returns:
-        ndarray: NumPy array representation of the geometry file.
+        NumPy array representation of the geometry file.
     """
     opener = gzip.open if compressed else open
     with opener(filename, "rb") as f:
@@ -130,9 +130,9 @@ def write(
     Args:
         filename (str): Filename of a geometry file.
         data (dict): Dictionary representation of a geometry file.
-        type (Type, optional): Data type to be written. Defaults to Type.EXTENDED.
-        compressed (bool, optional): True if file should be compressed, False otherwise.
-            Defaults to True.
+        type (Type, optional): Data type to be written. Defaults to `Type.EXTENDED`.
+        compressed (bool, optional): `True` if file should be compressed, `False` 
+            otherwise. Defaults to `True`.
     """
     array_data = _dict_to_ndarray(data, type)
     write_ndarray(filename, array_data, compressed)
@@ -144,8 +144,8 @@ def write_ndarray(filename: str, data: ndarray, compressed: bool = True):
     Args:
         filename (str): Filename of a geometry file.
         data (ndarray): NumPy array representation of a geometry file.
-        compressed (bool, optional): True if file should be compressed, False otherwise.
-            Defaults to True.
+        compressed (bool, optional): `True` if file should be compressed, `False`
+            otherwise. Defaults to `True`.
     """
     if not _validate_data_type(data):
         raise ValueError("Invalid data type")
@@ -180,7 +180,7 @@ def get_basic(
 def _get_basename(path: Path) -> Path:
     """Extract the basename from a binary filename.
 
-    A specific check for the '.mcr' extension is added due to historical naming
+    A specific check for the `.mcr` extension is added due to historical naming
     conventions related to the association of binary files and their geometry files.
     """
     if not path.name:

micpy/matplotlib.py

@@ -13,24 +13,23 @@ except ImportError:
 
 def _register_colormaps():
     colors = [
-        "#1102d8",
-        "#3007ba",
-        "#500b9d",
-        "#6f0e81",
-        "#8d1364",
-        "#ac1748",
-        "#cb1b2b",
-        "#ea1e0f",
-        "#f83605",
-        "#fa600f",
-        "#fb8817",
-        "#fdb120",
-        "#ffda29",
-        "#ffed4d",
-        "#fff380",
-        "#fffbb4",
+        "#1102d8",  # 17, 2, 216
+        "#3007ba",  # 48, 7, 186
+        "#500b9d",  # 80, 11, 157
+        "#6f0e81",  # 111, 14, 129
+        "#8d1364",  # 141, 19, 100
+        "#ac1748",  # 172, 23, 72
+        "#cb1b2b",  # 203, 27, 43
+        "#ea1e0f",  # 234, 30, 15
+        "#f83605",  # 248, 54, 5
+        "#fa600f",  # 250, 96, 15
+        "#fb8817",  # 251, 136, 23
+        "#fdb120",  # 253, 177, 32
+        "#ffda29",  # 255, 218, 41
+        "#ffed4d",  # 255, 237, 77
+        "#fff380",  # 255, 243, 128
+        "#fffbb4",  # 255, 251, 180
     ]
-
     version = LooseVersion(matplotlib.__version__) >= LooseVersion("3.7")
 
     create = matplotlib.colors.LinearSegmentedColormap.from_list

micpy/tab.py

@@ -1,4 +1,4 @@
-"""This module provides methods to read and parse tabular files."""
+"""The `micpy.tab` module provides methods to read and parse tabular files."""
 
 import io
 import re
@@ -20,15 +20,15 @@ def parse(
 
     Args:
         string (str): The content of a tabular file as a string.
-        parse_header (bool, optional): Whether to parse the header. Defaults to True.
+        parse_header (bool, optional): Whether to parse the header. Defaults to `True`.
         ignore_invalid_header (bool, optional): Whether to ignore invalid headers.
-            Defaults to True.
+            Defaults to `True`.
 
     Raises:
-        FormatError: If the number of columns in the header does not match the body.
+        `FormatError`: If the number of columns in the header does not match the body.
 
     Returns:
-        DataFrame: The content of the file as a pandas DataFrame.
+        The content of the file as a pandas DataFrame.
     """
     lines = string.splitlines()
     return _parse_lines(lines, parse_header, ignore_invalid_header)
@@ -41,15 +41,15 @@ def read(
 
     Args:
         filename (str): Path to the file.
-        parse_header (bool, optional): Whether to parse the header. Defaults to True.
+        parse_header (bool, optional): Whether to parse the header. Defaults to `True`.
         ignore_invalid_header (bool, optional): Whether to ignore invalid headers.
-            Defaults to True.
+            Defaults to `True`.
 
     Raises:
-        FormatError: If the number of columns in the header does not match the body.
+        `FormatError`: If the number of columns in the header does not match the body.
 
     Returns:
-        DataFrame: The content of the file as a pandas DataFrame.
+        The content of the file as a pandas DataFrame.
     """
     with open(filename, mode="r", encoding="utf8") as file:
         lines = file.readlines()

micpy/utils.py

@@ -4,6 +4,17 @@ import sys
 import time
 
 
+def convert_si(value, unit_in, unit_out):
+    """Convert value from one SI unit to another SI unit."""
+    SI = {"μm": 0.000001, "mm": 0.001, "cm": 0.01, "m": 1.0}
+
+    if isinstance(value, (float, int)):
+        return value * SI[unit_in] / SI[unit_out]
+    elif isinstance(value, (tuple, list)):
+        return [v * SI[unit_in] / SI[unit_out] for v in value]
+    raise ValueError("Unsupported value type.")
+
+
 def progress_indicator(iterable, description="Progress", unit="Iteration", start=1):
     """Progress indicator for iterable."""
 

micpy/version.py

@@ -1 +1 @@
-__version__ = "0.2.15b0"
+__version__ = "0.2.17b0"

{micress_micpy-0.2.15b0.dist-info → micress_micpy-0.2.17b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: micress-micpy
-Version: 0.2.15b0
+Version: 0.2.17b0
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de

micress_micpy-0.2.17b0.dist-info/RECORD

@@ -0,0 +1,12 @@
+micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
+micpy/bin.py,sha256=GzY0Gva3wp0n6vcKqv9yR3zzcg6ib1GtFzCKv8yXsR0,26777
+micpy/geo.py,sha256=pwMDSwG8i9XqmX2DWrSWuvtpni_Z7VLO586LNgEuORk,7366
+micpy/matplotlib.py,sha256=SLfk7H1v5L7H_L-a_FqobS0nKY3eSbFRF01h433SpVQ,2090
+micpy/tab.py,sha256=QCnfggxRWkKgS9-zGj8kyCjhfUw7QeTgGZWedHh4MTw,3548
+micpy/utils.py,sha256=-JS5SRqH4QMD6_pXBKPVw5zPNTbaqkcOUu9ej5Gi0QU,1282
+micpy/version.py,sha256=JOpzAb63fvBI_jPvlsPW3cGBI7CByIaM5IXZyr6SXOU,26
+micress_micpy-0.2.17b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
+micress_micpy-0.2.17b0.dist-info/METADATA,sha256=z2YjOYSHKOAtMtFk1NXS1bHkV31fKPHJcJZllNB1ZjQ,3824
+micress_micpy-0.2.17b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+micress_micpy-0.2.17b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
+micress_micpy-0.2.17b0.dist-info/RECORD,,

micress_micpy-0.2.15b0.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=0RB4FTad00sriZvQdHuTvkzT9D4_pLS_eFwpYS7EOhA,26492
-micpy/geo.py,sha256=dcXcxvAxPpe4Rrs1ImYs8H67c2228brabdefJMoLn0g,7354
-micpy/matplotlib.py,sha256=toxFTtTaA-usuWUltMp0XufQee4-n68XH7SN2In2NZY,1845
-micpy/tab.py,sha256=ZXhL6bg17W3jqFFX28htCOAV9W_W3op_-GD7iU5a_wY,3547
-micpy/utils.py,sha256=Kt1AvhMvWer9uftbb88X7N27aXtQdJl26grHmmm2vOQ,859
-micpy/version.py,sha256=tyiEmp3lrfZHINaXvAGtz6wbg_fRgizg1D1jsMt3PXo,26
-micress_micpy-0.2.15b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.2.15b0.dist-info/METADATA,sha256=Po-1cfNOIsV2m9wU_oj8kKzf2LllWQf-50PQD5O_g3c,3824
-micress_micpy-0.2.15b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.2.15b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.2.15b0.dist-info/RECORD,,