micress-micpy 0.2.13b4__py3-none-any.whl → 0.2.15b0__py3-none-any.whl

micpy/bin.py

@@ -5,6 +5,7 @@ from typing import Callable, IO, List, Tuple, Generator
 
 import gzip
 import os
+import sys
 import warnings
 import zlib
 
@@ -230,7 +231,7 @@ class Index(List[Position]):
     @staticmethod
     def from_file(
         file: IO[bytes],
-        show_progress: bool = True,
+        verbose: bool = True,
         chunk_size: int = Chunk.DEFAULT_SIZE,
         compressed: bool = True,
         position: Position = None,
@@ -240,7 +241,7 @@ class Index(List[Position]):
             file, chunk_size=chunk_size, compressed=compressed, position=position
         )
 
-        if show_progress:
+        if verbose:
             iterator = utils.progress_indicator(
                 iterator, description="Indexing", unit="Field"
             )
@@ -250,13 +251,13 @@ class Index(List[Position]):
     @staticmethod
     def from_filename(
         filename: str,
-        show_progress: bool = True,
+        verbose: bool = True,
         chunk_size: int = Chunk.DEFAULT_SIZE,
         compressed: bool = True,
     ):
         """Build an index from a binary file."""
         file = open(filename, "rb")
-        return Index.from_file(file, show_progress, chunk_size, compressed)
+        return Index.from_file(file, verbose, chunk_size, compressed)
 
 
 class Field(np.ndarray):
@@ -535,7 +536,7 @@ class FieldList(List[Field]):
             raise ImportError("matplotlib is not installed")
 
         if cols is None:
-            cols = int(np.sqrt(len(self)))
+            cols = int(np.ceil(np.sqrt(len(self))))
 
         rows = (len(self) + cols - 1) // cols
 
@@ -576,12 +577,14 @@ class File:
         self,
         filename: str,
         chunk_size: int = Chunk.DEFAULT_SIZE,
+        verbose: bool = True,
     ):
         """Initialize a binary 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.
 
         Raises:
             FileNotFoundError: If file is not found.
@@ -589,8 +592,9 @@ class File:
         if not os.path.isfile(filename):
             raise FileNotFoundError(f"File not found: {filename}")
 
-        self._filename = filename
+        self._filename: str = filename
         self._chunk_size: int = chunk_size
+        self._verbose: bool = verbose
 
         self._file: IO[bytes] = None
         self._compressed: bool = None
@@ -604,11 +608,8 @@ class File:
         try:
             self.find_geo()
         except (geo.GeometryFileNotFoundError, geo.MultipleGeometryFilesError):
-            print(
-                "Caution: A geometry file was not found. "
-                "To read a geometry from a designated location, use the read_geo() method. "
-                "Alternatively, you can manually set the geometry by executing set_geo()."
-            )
+            if self._verbose:
+                self._warn("Caution: A geometry file was not found.")
 
     def __getitem__(self, key: int or slice or list or Callable[[Field], bool]):
         return self.read(key)
@@ -622,73 +623,75 @@ class File:
     def __iter__(self):
         return self.iterate()
 
-    def open(self):
-        """Open the file."""
-        if not self._file:
-            self._file = open(self._filename, "rb")
-            self._compressed = utils.is_compressed(self._filename)
+    def _info(self, *args):
+        if self._verbose:
+            print(*args)
 
-        return self
+    def _warn(self, *args):
+        if self._verbose:
+            print(*args, file=sys.stderr)
 
-    def close(self):
-        """Close the file."""
+    def _open_file(self):
+        self._file = open(self._filename, "rb")
+        self._compressed = utils.is_compressed(self._filename)
+
+    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,
-        show_progress: bool = True,
-        create: bool = None,
-        update: bool = None,
-    ) -> Index:
-        """Build an index of the file.
-
-        Args:
-            show_progress (bool, optional): Show progress bar. Defaults to True.
-            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,
+    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,
-            show_progress=show_progress,
+            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.
@@ -748,7 +751,7 @@ class File:
         """Get a string representation of the geometry."""
 
         if self.shape is None or self.spacing is None:
-            print("Geometry: None")
+            self._info("Geometry: None")
             return
 
         dimensions = Field.dimensions(self.shape)
@@ -756,58 +759,57 @@ class File:
         spacing = np.round(self.spacing, 7)
         size = cells * spacing
 
-        print(
-            f"Geometry: {dimensions}-Dimensional Grid\n"
-            f"Grid Size: {tuple(size)}μm³\n"
-            f"Grid Shape (Cell Count): {tuple(cells)}\n"
-            f"Grid Spacing (Cell Size): {tuple(spacing)}μm³"
-        )
+        self._info(f"Geometry: {dimensions}-Dimensional Grid")
+        self._info(f"Grid Size: {tuple(size)}μm³")
+        self._info(f"Grid Shape (Cell Count): {tuple(cells)}")
+        self._info(f"Grid Spacing (Cell Size): {tuple(spacing)}μm³")
 
-    def iterate(self, show_progress: bool = True):
+    def iterate(self):
         """Iterate over fields in the file.
 
-        Args:
-            show_progress (bool, optional): Show progress bar. Defaults to True.
-
         Returns:
             Field: Field data.
         """
-        for position in self.index(show_progress=show_progress):
+        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,
-        show_progress: bool = True,
-    ):
+    def read(self, key: int or slice or list or Callable[[Field], bool] = None):
         """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.
-            show_progress (bool, optional): Show progress bar. Defaults to True.
 
         Returns:
-            Field: Field data.
+            FieldList: List of fields.
         """
 
         def read_field(self, field_id: int or slice or list):
             position = self._index[field_id]
             return Field.read(position, shape=self.shape, spacing=self.spacing)
 
-        self.index(show_progress=show_progress)
+        def iterable(iterable):
+            if self._verbose:
+                return utils.progress_indicator(
+                    iterable, description="Reading", unit="Field"
+                )
+            return iterable
+
+        self.index()
 
         if key is None:
-            return FieldList(self.iterate())
-        if isinstance(key, int):
-            return read_field(self, key)
-        if isinstance(key, slice):
-            start, stop, step = key.start, key.stop, key.step
-            key = list(range(len(self._index))[start:stop:step])
-        if isinstance(key, list):
-            return FieldList([read_field(self, i) for i in key])
-        if isinstance(key, Callable):
-            return FieldList([field for field in self.iterate() if key(field)])
-
-        raise TypeError("Invalid argument type")
+            fields = list(field for field in iterable(self.iterate()))
+        elif isinstance(key, int):
+            fields = [read_field(self, key)]
+        elif isinstance(key, slice):
+            indices = range(*key.indices(len(self._index)))
+            fields = [read_field(self, i) for i in iterable(indices)]
+        elif isinstance(key, list):
+            fields = [read_field(self, 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 FieldList(fields)

micpy/utils.py

@@ -8,19 +8,22 @@ def progress_indicator(iterable, description="Progress", unit="Iteration", start
     """Progress indicator for iterable."""
 
     start_time = time.time()
+
     for i, item in enumerate(iterable, start=start):
         yield item
+
         elapsed_time = time.time() - start_time
         average_time = elapsed_time / i
 
-        print(
-            f"\r{description}: {unit} {i}. Elapsed Time: {elapsed_time:.2f}s. Average Time/{unit}: {average_time:.2f}s",
-            end="",
-        )
-        # The print method's flush is not guaranteed to work in IPython environments. A
-        # workaround is to use sys.stdout.flush() instead.
+        message = f"\r{description}: {unit} {i}. Elapsed Time: {elapsed_time:.2f}s. Average Time/{unit}: {average_time:.2f}s"
+
+        sys.stdout.write("\r\x1b[0K")  # Clear line
+        print(message, end="")
         sys.stdout.flush()
 
+    print("")
+    sys.stdout.flush()
+
 
 def is_compressed(filename):
     """Check if a file is compressed."""

micpy/version.py

@@ -1 +1 @@
-__version__ = "0.2.13b4"
+__version__ = "0.2.15b0"

{micress_micpy-0.2.13b4.dist-info → micress_micpy-0.2.15b0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: micress-micpy
-Version: 0.2.13b4
+Version: 0.2.15b0
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de
@@ -59,6 +59,7 @@ for field in bin.File("A001_Delta_Gamma.conc1"):
 #### Read all fields
 
 ```python
+
 from micpy import bin
 
 with bin.File("A001_Delta_Gamma.conc1") as file:

micress_micpy-0.2.15b0.dist-info/RECORD

@@ -0,0 +1,12 @@
+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,,

micress_micpy-0.2.13b4.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=k75S6izFjBmNohjjHm-DEOSYp5eCl_iWi_bs-4OFjlc,26530
-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=fN2FFRlhOnAe00fdrdGBJvhlPrfqIyIiWK9PY7HQaHQ,919
-micpy/version.py,sha256=4G2XnZ6DntBZ0cJueBhEVZgO2A-1Auou_W5b-24qWKk,26
-micress_micpy-0.2.13b4.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.2.13b4.dist-info/METADATA,sha256=7-5BHF15NtEdkxp8pO5Wj6JtAcj3P0TRR_-DfOQB_Q8,3822
-micress_micpy-0.2.13b4.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.2.13b4.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.2.13b4.dist-info/RECORD,,