micress-micpy 0.3.1b0__py3-none-any.whl → 0.3.1b2__py3-none-any.whl

micpy/bin.py

@@ -394,7 +394,7 @@ class Series(np.ndarray):
         obj.times = [field.time for field in fields]
         obj.spacings = [field.spacing for field in fields]
         return obj
-    
+
     def __array_finalize__(self, obj):
         if obj is None:
             return
@@ -403,34 +403,43 @@ class Series(np.ndarray):
         self.times = getattr(obj, "times", None)
         self.spacings = getattr(obj, "spacings", None)
 
-    def __iter__(self):
+    def iter_field(self):
+        """Iterate over fields in the series.
+
+        Yields:
+            Field.
+        """
         for item, time, spacing in zip(self, self.times, self.spacings):
             yield Field(item, time, spacing)
 
-    def get(self, index: Union[int, list, slice]) -> Field:
-        """Get one or more fields from the series.
+    def get_field(self, index: int) -> Field:
+        """Get a field from the series.
 
         Args:
-            index (Union[int, list, slice]): Index of the field.
+            index (int): Index of the field.
 
         Returns:
             Field.
         """
+        return Field(self[index], self.times[index], self.spacings[index])
 
-        if isinstance(index, int):
-            return Field(self[index], self.times[index], self.spacings[index])
-        elif isinstance(index, slice):
-            series = self[index]
-            series.times = self.times[index]
-            series.spacings = self.spacings[index]
-            return series
-        elif isinstance(index, list):
-            series = self[index]
-            series.times = [self.times[i] for i in index]
-            series.spacings = [self.spacings[i] for i in index]
-            return series
-        raise TypeError("Invalid argument type")
+    def get_series(self, key: Union[int, slice, list]) -> "Series":
+        """Get a series of fields.
 
+        Args:
+            key (Union[int, slice, list]): Key to list of field IDs, a slice object, or a
+                list of field IDs.
+
+        Returns:
+            Series of fields.
+        """
+        if isinstance(key, int):
+            return Series([self.get_field(key)])
+        if isinstance(key, slice):
+            return Series([self.get_field(i) for i in range(*key.indices(len(self)))])
+        if isinstance(key, list):
+            return Series([self.get_field(i) for i in key])
+        raise TypeError("Invalid argument type")
 
     def write(self, filename: str, compressed: bool = True, geometry: bool = True):
         """Write the series to a binary file.
@@ -445,7 +454,7 @@ class Series(np.ndarray):
 
         file_open = gzip.open if compressed else open
         with file_open(filename, "wb") as file:
-            for field in self:
+            for field in self.iter_field():
                 field.to_file(file, geometry)
                 geometry = False
 
@@ -588,8 +597,8 @@ class File:
         """Set the geometry.
 
         Args:
-            shape (Tuple[int, int, int]): Shape of the geometry.
-            spacing (Tuple[float, float, float]): Spacing of the geometry in μm.
+            shape (Tuple[int, int, int]): Shape of the geometry (z, y, x).
+            spacing (Tuple[float, float, float]): Spacing of the geometry (dz, dy, dx) in μm.
         """
 
         self.shape = np.array(shape)
@@ -610,8 +619,8 @@ class File:
 
         geometry = geo.read(filename, type=geo.Type.BASIC, compressed=compressed)
 
-        shape = geometry["shape"]
-        spacing = geometry["spacing"]
+        shape = geometry["shape"][::-1]
+        spacing = geometry["spacing"][::-1]
 
         self.set_geometry(shape, spacing)
 
@@ -656,24 +665,34 @@ class File:
         for position in self.index():
             yield Field.read(position, shape=self.shape, spacing=self.spacing)
 
+    def read_field(self, field_id: int) -> Field:
+        """Read a field from the file.
+
+        Args:
+            field_id (int): Field ID.
+
+        Returns:
+            Field.
+        """
+        self.index()
+
+        position = self._index[field_id]
+        return Field.read(position, shape=self.shape, spacing=self.spacing)
+
     def read(
         self, key: Optional[Union[int, slice, list, Callable[[Field], bool]]] = None
     ) -> Series:
-        """Read field data from the file.
+        """Read a series of fields from the file.
 
         Args:
-            key (Union[int, slice, list, Callable[[Field], bool], optional): Key to
-                list of field IDs, a slice object, or a condition function.
-                Defaults to `None`.
+            key (Union[int, slice, list, Callable[[Field], bool]]): Key to list of
+            field IDs, a slice object, a list of field IDs, or a function that filters
+            fields. Defaults to `None`.
 
         Returns:
-            A series of fields.
+            Series of fields.
         """
 
-        def read_field(self, field_id: Union[int, slice, list]):
-            position = self._index[field_id]
-            return Field.read(position, shape=self.shape, spacing=self.spacing)
-
         def iterable(iterable):
             if self._verbose:
                 return utils.progress_indicator(
@@ -686,17 +705,16 @@ class File:
         if key is None:
             fields = list(field for field in iterable(self.iterate()))
         elif isinstance(key, int):
-            fields = [read_field(self, key)]
+            fields = [self.read_field(key)]
         elif isinstance(key, slice):
             indices = range(*key.indices(len(self._index)))
-            fields = [read_field(self, i) for i in iterable(indices)]
+            fields = [self.read_field(i) for i in iterable(indices)]
         elif isinstance(key, list):
-            fields = [read_field(self, i) for i in iterable(key)]
+            fields = [self.read_field(i) for i in iterable(key)]
         elif isinstance(key, Callable):
             fields = [field for field in iterable(self.iterate()) if key(field)]
         else:
             raise TypeError("Invalid argument type")
-
         return Series(fields)
 
 
@@ -755,7 +773,7 @@ def plot(
 
     if axis not in ["x", "y", "z"]:
         raise ValueError("Invalid axis")
-    
+
     if field.ndim != 3:
         raise ValueError("Invalid field shape")
 
@@ -768,8 +786,6 @@ def plot(
     elif axis == "y":
         x, y = "x", "z"
         slice_2d = field[:, index, :]
-        if Field.dimensions(field.shape) == 2:
-            slice_2d = slice_2d.reshape(slice_2d.shape[1], slice_2d.shape[0])
     elif axis == "x":
         x, y = "y", "z"
         slice_2d = field[:, :, index]

micpy/geo.py

@@ -165,8 +165,8 @@ def build(
 
     Args:
         filename (str): Filename of a binary file.
-        shape (tuple): Shape of the geometry.
-        spacing (tuple): Spacing of the geometry.
+        shape (tuple): Shape of the geometry (z, y, x).
+        spacing (tuple): Spacing of the geometry (dz, dy, dx) in μm.
     """
     geo_filename = _get_basename(Path(filename)).with_suffix(".geoF")
     geo_data = {

micpy/version.py

@@ -1 +1 @@
-__version__ = "0.3.1b0"
+__version__ = "0.3.1b2"

{micress_micpy-0.3.1b0.dist-info → micress_micpy-0.3.1b2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: micress-micpy
-Version: 0.3.1b0
+Version: 0.3.1b2
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de

micress_micpy-0.3.1b2.dist-info/RECORD

@@ -0,0 +1,12 @@
+micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
+micpy/bin.py,sha256=MbAzv-CXMUXZ8a8gynOQKCQIrOVrhuxL6fSl5wXcH0s,26117
+micpy/geo.py,sha256=z7dP3hC2Fhed4N5eRrlWlC4jtIXiYPIx2BYNhn10dfw,7447
+micpy/matplotlib.py,sha256=GF2ghyBORC5RRjW00DdsHu5aSkpMFdI9wqg6d_psPsI,1198
+micpy/tab.py,sha256=QCnfggxRWkKgS9-zGj8kyCjhfUw7QeTgGZWedHh4MTw,3548
+micpy/utils.py,sha256=Kt1AvhMvWer9uftbb88X7N27aXtQdJl26grHmmm2vOQ,859
+micpy/version.py,sha256=mAuhwKKFzwoBU7u49qo92gTigQagh5Nq5rzbLuYGQbI,25
+micress_micpy-0.3.1b2.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
+micress_micpy-0.3.1b2.dist-info/METADATA,sha256=E4qysyzpM5PH13fhB2MnOQao1XNVOKDp8hCT7fJUah8,1229
+micress_micpy-0.3.1b2.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+micress_micpy-0.3.1b2.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
+micress_micpy-0.3.1b2.dist-info/RECORD,,

micress_micpy-0.3.1b0.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=3xclBJLbbBW9N8w9izFEgFh3S2yKgYzrdQKjJsXftSU,25831
-micpy/geo.py,sha256=lVRTtPnTEykkSXNyLm3wnxXOwz72PFu0Spv8ZGHyUHo,7417
-micpy/matplotlib.py,sha256=GF2ghyBORC5RRjW00DdsHu5aSkpMFdI9wqg6d_psPsI,1198
-micpy/tab.py,sha256=QCnfggxRWkKgS9-zGj8kyCjhfUw7QeTgGZWedHh4MTw,3548
-micpy/utils.py,sha256=Kt1AvhMvWer9uftbb88X7N27aXtQdJl26grHmmm2vOQ,859
-micpy/version.py,sha256=o80l_DIF5j_g0KFIiC8SP5DtyipTIK4_NRfkjHjz1Mk,25
-micress_micpy-0.3.1b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.3.1b0.dist-info/METADATA,sha256=UFUfB1rNxBQxj1OlMO9Qo3YX92weqibYc59tujF8lBo,1229
-micress_micpy-0.3.1b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.3.1b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.3.1b0.dist-info/RECORD,,