micress-micpy 0.3.0b0__py3-none-any.whl → 0.3.1b1__py3-none-any.whl

micpy/bin.py

@@ -388,47 +388,48 @@ class Field(np.ndarray):
             self.to_file(file, geometry)
 
 
-class Series:
-    def __init__(self, fields: List[Field]):
-        self.stack = np.stack(fields)
-        self.times = [field.time for field in fields]
-        self.spacings = [field.spacing for field in fields]
+class Series(np.ndarray):
+    def __new__(cls, fields: List[Field]):
+        obj = np.asarray(fields).view(cls)
+        obj.times = [field.time for field in fields]
+        obj.spacings = [field.spacing for field in fields]
+        return obj
 
-    def __array__(self):
-        return self.stack
+    def __array_finalize__(self, obj):
+        if obj is None:
+            return
 
-    def __len__(self):
-        return len(self.stack)
+        # pylint: disable=attribute-defined-outside-init
+        self.times = getattr(obj, "times", None)
+        self.spacings = getattr(obj, "spacings", None)
 
     def __iter__(self):
-        for item, time, spacing in zip(self.stack, self.times, self.spacings):
+        for item, time, spacing in zip(self, self.times, self.spacings):
             yield Field(item, time, spacing)
 
-    def __getitem__(self, index):
-        if isinstance(index, int):
-            return Field(self.stack[index], self.times[index], self.spacings[index])
-        elif isinstance(index, slice):
-            return Series(
-                [
-                    Field(item, time, spacing)
-                    for item, time, spacing in zip(
-                        self.stack[index], self.times[index], self.spacings[index]
-                    )
-                ]
-            )
-        raise TypeError("Invalid argument type")
+    def get(self, index: Union[int, list, slice]) -> Field:
+        """Get one or more fields from the series.
 
-    def __getattr__(self, name):
-        return getattr(self.stack, name)
-
-    def __dir__(self) -> List[str]:
-        return list(set(dir(type(self)) + dir(self.stack)))
+        Args:
+            index (Union[int, list, slice]): Index of the field.
 
-    def __repr__(self):
-        return repr(self.stack)
+        Returns:
+            Field.
+        """
 
-    def __str__(self):
-        return str(self.stack)
+        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 write(self, filename: str, compressed: bool = True, geometry: bool = True):
         """Write the series to a binary file.
@@ -586,8 +587,8 @@ 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 μm³.
+            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)
@@ -608,8 +609,8 @@ 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)
 
@@ -641,9 +642,9 @@ class File:
         size = cells * spacing
 
         self._info(f"Geometry: {dimensions}-Dimensional Grid")
-        self._info(f"Grid Size: {tuple(size)}μm³")
+        self._info(f"Grid Size [μm]: {tuple(size)}")
         self._info(f"Grid Shape (Cell Count): {tuple(cells)}")
-        self._info(f"Grid Spacing (Cell Size): {tuple(spacing)}μm³")
+        self._info(f"Grid Spacing (Cell Size) [μm]: {tuple(spacing)}")
 
     def iterate(self) -> Generator[Field, None, None]:
         """Iterate over fields in the file.
@@ -713,7 +714,7 @@ class PlotArgs:
         cax (matplotlib.Axes, optional): Axes of the color bar. 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): Colormap. Defaults to `
+        cmap (str, optional): Colormap. Defaults to `micpy`.
     """
 
     title: Optional[str] = None
@@ -754,6 +755,9 @@ def plot(
     if axis not in ["x", "y", "z"]:
         raise ValueError("Invalid axis")
 
+    if field.ndim != 3:
+        raise ValueError("Invalid field shape")
+
     if args is None:
         args = PlotArgs()
 
@@ -763,8 +767,6 @@ 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]
@@ -778,7 +780,8 @@ def plot(
     if args.title is not None:
         ax.set_title(args.title)
     else:
-        ax.set_title(f"t={np.round(field.time, 7)}s")
+        if isinstance(field, Field):
+            ax.set_title(f"t={np.round(field.time, 7)}s")
     if args.xlabel is not None:
         ax.set_xlabel(args.xlabel)
     else:

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__ = "0.3.0b0"
+__version__ = "0.3.1b1"

{micress_micpy-0.3.0b0.dist-info → micress_micpy-0.3.1b1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: micress-micpy
-Version: 0.3.0b0
+Version: 0.3.1b1
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de

micress_micpy-0.3.1b1.dist-info/RECORD

@@ -0,0 +1,12 @@
+micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
+micpy/bin.py,sha256=LQiaAxLCyBw_7kfimFbZtqqMoP3iAYFVKDc4Ohvyxm8,25729
+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=zKEPT4cdwsCB_uCEMo5TXBcz3hseWXYp71mYqedQBds,25
+micress_micpy-0.3.1b1.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
+micress_micpy-0.3.1b1.dist-info/METADATA,sha256=5oK-n39nupCZmnR1PNSesTpWkYhTFREiJFGAuY_mZ7g,1229
+micress_micpy-0.3.1b1.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
+micress_micpy-0.3.1b1.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
+micress_micpy-0.3.1b1.dist-info/RECORD,,

micress_micpy-0.3.0b0.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=6CiN1KUrIVDn5pXtf05n-A7D7yOFAUXAbfBUeXpgcGs,25521
-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=v6LLclreYkCiqxCP6QRdhtVAzCVndQ77c0lTMqPZjXk,25
-micress_micpy-0.3.0b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.3.0b0.dist-info/METADATA,sha256=RbN1IrUFx14nsUJB2fIeLxrxFD49sF1sujNg1vBmlpA,1229
-micress_micpy-0.3.0b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.3.0b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.3.0b0.dist-info/RECORD,,