micress-micpy 0.2.14b0__py3-none-any.whl → 0.2.16b0__py3-none-any.whl

micpy/bin.py

@@ -631,67 +631,67 @@ class File:
         if self._verbose:
             print(*args, file=sys.stderr)
 
-    def open(self):
-        """Open the file."""
-        if not self._file:
-            self._file = open(self._filename, "rb")
-            self._compressed = utils.is_compressed(self._filename)
-
-        return self
+    def _open_file(self):
+        self._file = open(self._filename, "rb")
+        self._compressed = utils.is_compressed(self._filename)
 
-    def close(self):
-        """Close the file."""
+    def _close_file(self):
         if self._file:
             self._file.close()
+        self._reset()
 
+    def _reset(self):
         self._file = None
         self._compressed = None
         self._created = None
         self._modified = None
         self._index = None
 
-    def index(self, create: bool = None, update: bool = None) -> Index:
-        """Build an index of the file.
-
-        Args:
-            create (bool, optional): Create the index. Defaults to None (auto).
-            update (bool, optional): Update the index. Defaults to None (auto).
+    def _update_timestamps(self):
+        self._created = os.path.getctime(self._filename)
+        self._modified = os.path.getmtime(self._filename)
 
-        Returns:
-            Index: Index of the file.
-        """
-
-        def file_created():
-            return self._created != os.path.getctime(self._filename)
-
-        def file_modified():
-            return self._modified != os.path.getmtime(self._filename)
-
-        create = create if create is not None else file_created()
-        update = update if update is not None else file_modified()
-
-        if create:
-            self.close()
-        self.open()
+    def open(self):
+        """Open the file."""
+        if not self._file:
+            self.create_index()
+        return self
 
-        if create or update:
-            self._created = os.path.getctime(self._filename)
-            self._modified = os.path.getmtime(self._filename)
+    def close(self):
+        """Close the file."""
+        self._close_file()
+
+    def index(self):
+        """Get the index of the file."""
+        if self._created != os.path.getctime(self._filename):
+            self.create_index()
+        elif self._modified != os.path.getmtime(self._filename):
+            self.update_index()
+        return self._index
 
-        index_params = dict(
-            file=self._file,
-            compressed=self._compressed,
-            chunk_size=self._chunk_size,
+    def create_index(self):
+        """Create an index of the file."""
+        self._close_file()
+        self._open_file()
+        self._update_timestamps()
+        self._index = Index.from_file(
+            self._file,
             verbose=self._verbose,
+            chunk_size=self._chunk_size,
+            compressed=self._compressed,
         )
 
-        if create:
-            self._index = Index.from_file(**index_params)
-        elif update:
-            index = Index.from_file(**index_params, position=self._index[-1])
-            self._index.extend(index)
-
-        return self._index
+    def update_index(self):
+        """Update the index of the file."""
+        self._update_timestamps()
+        index = Index.from_file(
+            self._file,
+            verbose=self._verbose,
+            chunk_size=self._chunk_size,
+            compressed=self._compressed,
+            position=self._index[-1],
+        )
+        self._index.extend(index)
 
     def times(self) -> List[float]:
         """Get the times of the fields in the file.
@@ -706,7 +706,7 @@ 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)
@@ -726,7 +726,11 @@ class File:
                 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.

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__ = "0.2.14b0"
+__version__ = "0.2.16b0"

{micress_micpy-0.2.14b0.dist-info → micress_micpy-0.2.16b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: micress-micpy
-Version: 0.2.14b0
+Version: 0.2.16b0
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de

micress_micpy-0.2.16b0.dist-info/RECORD

@@ -0,0 +1,12 @@
+micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
+micpy/bin.py,sha256=1eO8nv3j3CNFFx35W2I-MdOTgelxVwOf3AzIv5-cnXY,26586
+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=-JS5SRqH4QMD6_pXBKPVw5zPNTbaqkcOUu9ej5Gi0QU,1282
+micpy/version.py,sha256=MwwJ3Tq2WyMrlg5ARuI934Sn37GJtLQJ8y2GpYXfdw4,26
+micress_micpy-0.2.16b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
+micress_micpy-0.2.16b0.dist-info/METADATA,sha256=ZtkZWKBm6rCf4Bgwq8hKzO-sEdNkSpCBe7XDC5sF6EY,3824
+micress_micpy-0.2.16b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+micress_micpy-0.2.16b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
+micress_micpy-0.2.16b0.dist-info/RECORD,,

micress_micpy-0.2.14b0.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=VHh9JPJAr0jjFJnyPLO-kIO1AdEuQgBun8oakLOpaoM,26534
-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=hNVzjX1MyH60RwPXe8_zwZd7WsxPBh2PKFtmqeYKn_Y,26
-micress_micpy-0.2.14b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.2.14b0.dist-info/METADATA,sha256=2kD96oel2I-27Of19SvAh6kKYTpKrNInKrR9pw0nwtY,3824
-micress_micpy-0.2.14b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.2.14b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.2.14b0.dist-info/RECORD,,