micress-micpy 0.3.2b0__py3-none-any.whl → 0.4.0a1__py3-none-any.whl

micpy/paraview_plugin.py

@@ -0,0 +1,221 @@
+from __future__ import annotations
+
+from typing import Dict, List, Optional, Tuple
+
+import vtk
+from vtkmodules.vtkCommonExecutionModel import vtkStreamingDemandDrivenPipeline
+from vtkmodules.util.vtkAlgorithm import VTKPythonAlgorithmBase
+
+from micpy import bin as micpy_bin
+from micpy import vtk as micpy_vtk
+
+
+class MicressBinaryReader(VTKPythonAlgorithmBase):
+    """ParaView reader for MICRESS binary files via MicPy."""
+
+    def __init__(self):
+        super().__init__(nInputPorts=0, nOutputPorts=1, outputType="vtkImageData")
+
+        self._filename: Optional[str] = None
+        self._file: Optional[micpy_bin.File] = None
+
+        self._array_name: str = "values"
+
+        self._cached_meta: Optional[
+            Tuple[
+                Tuple[int, int, int, int, int, int],
+                Tuple[float, float, float],
+                Tuple[float, float, float],
+            ]
+        ] = None  # (extent6, spacing3, origin3)
+
+        self._times: List[float] = []
+        self._time_to_index: Dict[float, int] = {}
+
+    def SetFileName(self, filename: str) -> None:
+        filename = str(filename)
+        if filename == self._filename:
+            return
+        self._filename = filename
+        self._reset()
+        self.Modified()
+
+    def SetArrayName(self, name: str) -> None:
+        name = str(name) if name else "values"
+        if name == self._array_name:
+            return
+        self._array_name = name
+        self.Modified()
+
+    def _reset(self) -> None:
+        if self._file is not None:
+            try:
+                self._file.close()
+            except Exception:
+                pass
+        self._file = None
+        self._cached_meta = None
+        self._times = []
+        self._time_to_index = {}
+
+    def _open(self) -> None:
+        if self._file is None:
+            if not self._filename:
+                raise RuntimeError("No filename set.")
+            self._file = micpy_bin.File(self._filename).open()
+
+    def _ensure_meta(self) -> None:
+        if self._cached_meta is not None:
+            return
+        self._open()
+
+        field0 = self._file._read_field(0)
+        image0 = micpy_vtk.to_image(field0, name=self._array_name)
+
+        extent = tuple(int(x) for x in image0.GetExtent())
+        spacing = tuple(float(x) for x in image0.GetSpacing())
+        origin = tuple(float(x) for x in image0.GetOrigin())
+
+        self._cached_meta = (extent, spacing, origin)
+
+    def _ensure_times(self) -> None:
+        if self._times:
+            return
+        self._open()
+
+        times: List[float] = []
+        time_to_index: Dict[float, int] = {}
+
+        i = 0
+        while True:
+            try:
+                fld = self._file._read_field(i)
+            except (IndexError, EOFError):
+                break
+
+            tt = float(fld.time)
+            times.append(tt)
+            if tt not in time_to_index:
+                time_to_index[tt] = i
+            i += 1
+
+        self._times = times
+        self._time_to_index = time_to_index
+
+        # Temporary debug (prints to ParaView output console)
+        print(
+            "MicressBinaryReader: discovered",
+            len(self._times),
+            "timesteps:",
+            self._times,
+        )
+
+    def _get_index_for_requested_time(
+        self, req_t: Optional[float]
+    ) -> Tuple[int, float]:
+        self._ensure_times()
+
+        if not self._times:
+            return 0, 0.0
+
+        if req_t is None:
+            chosen_t = self._times[0]
+            return 0, float(chosen_t)
+
+        req_t = float(req_t)
+        chosen_t = min(self._times, key=lambda x: abs(x - req_t))
+        idx = self._time_to_index.get(chosen_t)
+        if idx is None:
+            idx = self._times.index(chosen_t)
+        return int(idx), float(chosen_t)
+
+    def _read_image_at_index(self, idx: int) -> vtk.vtkImageData:
+        self._open()
+        field = self._file._read_field(idx)
+        image = micpy_vtk.to_image(field, name=self._array_name)
+        return image
+
+    def RequestInformation(self, request, inInfo, outInfo):
+        if not self._filename:
+            return 1
+
+        self._ensure_meta()
+        self._ensure_times()
+
+        info = outInfo.GetInformationObject(0)
+
+        extent, spacing, origin = self._cached_meta
+        info.Set(vtkStreamingDemandDrivenPipeline.WHOLE_EXTENT(), extent, 6)
+        info.Set(vtk.vtkDataObject.SPACING(), spacing, 3)
+        info.Set(vtk.vtkDataObject.ORIGIN(), origin, 3)
+
+        if self._times:
+            ts = [float(x) for x in self._times]
+            vtkStreamingDemandDrivenPipeline.TIME_STEPS().Set(info, ts, len(ts))
+
+            tr = [float(min(ts)), float(max(ts))]
+            vtkStreamingDemandDrivenPipeline.TIME_RANGE().Set(info, tr, 2)
+
+        return 1
+
+    def RequestData(self, request, inInfo, outInfo):
+        if not self._filename:
+            raise RuntimeError("No filename set.")
+
+        self._ensure_meta()
+
+        info = outInfo.GetInformationObject(0)
+        output = vtk.vtkImageData.GetData(outInfo, 0)
+
+        req_t = None
+        if info.Has(vtkStreamingDemandDrivenPipeline.UPDATE_TIME_STEP()):
+            req_t = float(info.Get(vtkStreamingDemandDrivenPipeline.UPDATE_TIME_STEP()))
+
+        idx, chosen_t = self._get_index_for_requested_time(req_t)
+        image = self._read_image_at_index(idx)
+
+        extent, spacing, origin = self._cached_meta
+        output.SetExtent(extent)
+        output.SetSpacing(spacing)
+        output.SetOrigin(origin)
+        output.AllocateScalars(image.GetScalarType(), 0)
+
+        output.GetPointData().ShallowCopy(image.GetPointData())
+        output.GetCellData().ShallowCopy(image.GetCellData())
+        output.Modified()
+
+        output.GetInformation().Set(vtk.vtkDataObject.DATA_TIME_STEP(), float(chosen_t))
+
+        return 1
+
+
+try:
+    from paraview.util.vtkAlgorithm import smproxy, smproperty, smdomain
+except Exception:
+    smproxy = smproperty = smdomain = None
+
+if smproxy is not None:
+
+    @smproxy.reader(
+        name="MicressBinaryReader",
+        label="Micress Binary Reader (MicPy)",
+        extensions="mcr conc1 conc2 conc3 conc4 conc5 conc6 conc7 conc8 conc9 frac0 frac1 frac2 frac3 frac4 frac5 frac6 frac7 frac8 frac9 korn intf orie phas",
+        file_description="MICRESS Binary Files",
+    )
+    class _MicressBinaryReader(MicressBinaryReader):
+
+        @smproperty.stringvector(
+            name="FileName",
+            command="SetFileName",
+            number_of_elements=1,
+            panel_visibility="default",
+        )
+        @smdomain.filelist()
+        def FileName(self):
+            return [self._filename or ""]
+
+        @smproperty.stringvector(
+            name="ArrayName", command="SetArrayName", number_of_elements=1
+        )
+        def ArrayName(self):
+            return [self._array_name]

micpy/paraview_plugin_stub.py

@@ -0,0 +1 @@
+import micpy.paraview_plugin.reader

micpy/version.py

@@ -1 +1 @@
-__version__ = "0.3.2b0"
+__version__ = "0.4.0a1"

micpy/vtk.py

@@ -0,0 +1,60 @@
+from pathlib import Path
+
+import numpy as np
+import vtk
+from vtkmodules.util.numpy_support import numpy_to_vtk
+
+from micpy.bin import Field
+
+
+def to_image(
+    field: Field,
+    name: str = "values",
+):
+    a = np.asarray(field)
+    if a.ndim != 3:
+        raise ValueError("field must be 3D (nz, ny, nx)")
+
+    nz, ny, nx = a.shape
+    dz, dy, dx = field.spacing
+
+    image = vtk.vtkImageData()
+    image.SetOrigin(0.0, 0.0, 0.0)
+    image.SetSpacing(float(dx), float(dy), float(dz))
+    image.SetDimensions(nx + 1, ny + 1, nz + 1)
+
+    if not a.flags["C_CONTIGUOUS"]:
+        a = np.ascontiguousarray(a)
+
+    a_vtk = np.ndarray(shape=(nx, ny, nz), dtype=a.dtype, buffer=a, order="F")
+
+    flat_view = a_vtk.ravel(order="F")
+
+    arr = numpy_to_vtk(flat_view, deep=True)
+    arr.SetName(name)
+    image.GetCellData().SetScalars(arr)
+
+    return image
+
+
+def save_vti(
+    field: Field,
+    filename: str,
+    name: str = "values",
+) -> str:
+    image = to_image(field, name=name)
+
+    filename = str(Path(filename).with_suffix(".vti"))
+
+    writer = vtk.vtkXMLImageDataWriter()
+    writer.SetFileName(filename)
+
+    writer.SetInputData(image)
+    writer.SetDataModeToAppended()
+    writer.EncodeAppendedDataOff()
+
+    ok = writer.Write()
+    if ok != 1:
+        raise OSError(f"Failed to write {filename}")
+
+    return filename

{micress_micpy-0.3.2b0.dist-info → micress_micpy-0.4.0a1.dist-info}/METADATA

@@ -1,10 +1,10 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: micress-micpy
-Version: 0.3.2b0
+Version: 0.4.0a1
 Summary: MicPy is a Python package to facilitate MICRESS workflows.
 Author: Lukas Koschmieder
 Author-email: l.koschmieder@access-technology.de
-License: BSD-3-Clause (Copyright (c) 2024 Access e.V.)
+License: BSD-3-Clause (Copyright (c) 2024-2026 Access e.V.)
 Keywords: MICRESS
 Classifier: Development Status :: 4 - Beta
 Classifier: Intended Audience :: Science/Research
@@ -16,6 +16,18 @@ Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: matplotlib
 Requires-Dist: pandas
+Requires-Dist: rapidgzip
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: keywords
+Dynamic: license
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
 
 <center>
 
@@ -40,6 +52,7 @@ MicPy requires the following dependencies:
 - Python (>= 3.9)
 - Pandas (>= 1.1)
 - Matplotlib (>= 3) as an optional dependency for plotting
+- VTK (>= 9) as an optional dependency for 3D visualization
 
 ## Documentation
 

micress_micpy-0.4.0a1.dist-info/RECORD

@@ -0,0 +1,18 @@
+micpy/MicressBinaryReader copy.py,sha256=2LEgaL1hn5Azgu-itGtgKj7fK6naAAGKkzmN2sjItv4,4382
+micpy/MicressBinaryReader.py,sha256=1c-RGmKNmCR7LH1BVXJTx2IdeJ0vE_KS1bkpfQ0VJ_E,8540
+micpy/__init__.py,sha256=tM_wXPVfBznC9YIhVK1iukTkqW-Vg2OegKPGki12xb4,63
+micpy/bin copy.py,sha256=-cT-Xkih_jJmGbjKx4ahdWC8Y30lfudbCVGekXgccaE,26912
+micpy/bin.py,sha256=W7ksqCKRwTPvaMSUyPAWyUuN1WAUMg3sr7QmIkmINOw,26085
+micpy/geo.py,sha256=z7dP3hC2Fhed4N5eRrlWlC4jtIXiYPIx2BYNhn10dfw,7447
+micpy/matplotlib.py,sha256=GF2ghyBORC5RRjW00DdsHu5aSkpMFdI9wqg6d_psPsI,1198
+micpy/paraview_plugin.py,sha256=bN9KnoNp5eToiKDyBxi4qtDQFF1Yy_tKmFOAJEGdGDk,7010
+micpy/paraview_plugin_stub.py,sha256=GovBBOLZnJ-_csPvrJDu2cTj7qnHNnhbQPX1yxm7aY0,37
+micpy/tab.py,sha256=QCnfggxRWkKgS9-zGj8kyCjhfUw7QeTgGZWedHh4MTw,3548
+micpy/utils.py,sha256=Kt1AvhMvWer9uftbb88X7N27aXtQdJl26grHmmm2vOQ,859
+micpy/version.py,sha256=LP80qjLpeagualL_zMvkW8O_mhv-NwTuvnzc_4bOmK4,25
+micpy/vtk.py,sha256=48VB0pORhVkXqVHY4F8XdyfBlChyNl_OJWqQ5XK7mdY,1388
+micress_micpy-0.4.0a1.dist-info/licenses/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
+micress_micpy-0.4.0a1.dist-info/METADATA,sha256=2P0y6lKMyU-NhgBimydwpd_GU33kjqho7qycm3YmNiw,1567
+micress_micpy-0.4.0a1.dist-info/WHEEL,sha256=qELbo2s1Yzl39ZmrAibXA2jjPLUYfnVhUNTlyF1rq0Y,92
+micress_micpy-0.4.0a1.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
+micress_micpy-0.4.0a1.dist-info/RECORD,,

{micress_micpy-0.3.2b0.dist-info → micress_micpy-0.4.0a1.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: bdist_wheel (0.41.2)
+Generator: setuptools (80.10.1)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

micress_micpy-0.3.2b0.dist-info/RECORD

@@ -1,12 +0,0 @@
-micpy/__init__.py,sha256=7wQUaseppjQYZW1iAVNm2WSDjvBLlqtY8tiHsfDaW5Q,148
-micpy/bin.py,sha256=5_VjciuoY7MGgbsYGD4YEBsGIRtN1UHEu1bF4c84KoU,26150
-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=cmRz06nS65Gsdx46NbGK09hWYOtmDwCXP9-XRCvNvUc,25
-micress_micpy-0.3.2b0.dist-info/LICENSE,sha256=seHdCiArizUoWZ6bEFg6N3K2ZtfPK35wvOwg0kH-f6o,1488
-micress_micpy-0.3.2b0.dist-info/METADATA,sha256=iJ3JJYKKdZzkdnCkfYstoSu4NDaYJMX0aIAuMKIFoQs,1229
-micress_micpy-0.3.2b0.dist-info/WHEEL,sha256=yQN5g4mg4AybRjkgi-9yy4iQEFibGQmlz78Pik5Or-A,92
-micress_micpy-0.3.2b0.dist-info/top_level.txt,sha256=RiopkpW0AGNYdtOW2eQUWgm3yHGC13q9pWlHb2alhiE,6
-micress_micpy-0.3.2b0.dist-info/RECORD,,