fdsreader 1.2.8__tar.gz → 1.3.7__tar.gz

{fdsreader-1.2.8/fdsreader.egg-info → fdsreader-1.3.7}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: fdsreader
-Version: 1.2.8
+Version: 1.3.7
 Summary: Python reader for data generated by FDS.
-Home-page: https://github.com/JanVogelsang/fdsreader
+Home-page: https://github.com/FireDynamics/fdsreader
 Author: FZJ IAS-7 (Prof. Dr. Lukas Arnold, Jan Vogelsang)
 Author-email: j.vogelsang@fz-juelich.de
 License: UNKNOWN

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/_version.py

@@ -7,5 +7,5 @@ Provides fdsreader version information.
 
 from incremental import Version
 
-__version__ = Version('fdsreader', 1, 2, 8)
+__version__ = Version('fdsreader', 1, 3, 7)
 __all__ = ["__version__"]

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/bndf/obstruction.py

@@ -149,7 +149,7 @@ class SubObstruction:
 
     :ivar extent: :class:`Extent` object containing 3-dimensional extent information.
     :ivar bound_indices: Indices used to define obstruction bounds in terms of mesh locations.
-    :ivar side_surfaces: Tuple of six :class:`Surface`s for each side of the cuboid.
+    :ivar side_surfaces: Tuple of six :class:`Surface` s for each side of the cuboid.
     :ivar hide_times: List with points in time from when on the SubObstruction will be hidden.
     :ivar show_times: List with points in time from when on the SubObstruction will be shown.
     """
@@ -177,6 +177,10 @@ class SubObstruction:
         if not settings.LAZY_LOAD:
             _ = self._boundary_data[bid].data
 
+    @property
+    def has_boundary_data(self):
+        return len(self._boundary_data) != 0
+
     def get_data(self, quantity: Union[str, Quantity]):
         if type(quantity) == Quantity:
             quantity = quantity.name
@@ -304,7 +308,7 @@ class Obstruction:
         if type(quantity) == Quantity:
             quantity = quantity.name
 
-        ret = [subobst.get_data(quantity) for subobst in self._subobstructions]
+        ret = [subobst.get_data(quantity) for subobst in self._subobstructions if subobst.has_boundary_data]
         if orientation == 0:
             return ret
         return [bndf for bndf in ret if orientation in bndf.data.keys()]
@@ -313,7 +317,7 @@ class Obstruction:
     def has_boundary_data(self):
         """Whether boundary data has been output in the simulation.
         """
-        return len(self._subobstructions[0]._boundary_data) != 0
+        return any(subobst.has_boundary_data for subobst in self._subobstructions)
 
     def clear_cache(self):
         """Remove all data from the internal cache that has been loaded so far to free memory.

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/evac/EvacCollection.py

@@ -287,6 +287,7 @@ class EvacCollection(FDSDataCollection):
     def _load_eff_data(self):
         file_path = self._base_path + ".eff"
         if not os.path.exists(file_path):
+            self._eff = None
             return
 
         with open(file_path, 'rb') as infile:

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/evac/evacuation.py

@@ -66,7 +66,7 @@ class Evacuation:
         self.lower_bounds = {q.name: [] for q in self.quantities}
         self.upper_bounds = {q.name: [] for q in self.quantities}
 
-        self._init_callback = None
+        self._init_callback = lambda: None
 
     @property
     def id(self):

fdsreader-1.3.7/fdsreader/export/__init__.py

@@ -0,0 +1,3 @@
+from .smoke3d_exporter import export_smoke_raw
+from .slcf_exporter import export_slcf_raw
+from .obst_exporter import export_obst_raw

fdsreader-1.3.7/fdsreader/export/obst_exporter.py

@@ -0,0 +1,116 @@
+import os
+from pathlib import Path
+import numpy as np
+from typing_extensions import Literal
+from ..bndf import Obstruction
+from ..bndf.utils import sort_patches_cartesian
+
+
+def export_obst_raw(obst: Obstruction, output_dir: str, ordering: Literal['C', 'F'] = 'C'):
+    """Exports the 3d arrays to raw binary files with corresponding .yaml meta files.
+
+    :param smoke3d: The :class:`Smoke3D` object to export.
+    :param output_dir: The directory in which to save all files.
+    :param ordering: Whether to write the data in C or Fortran ordering.
+    """
+    from pathos.pools import ProcessPool as Pool
+    from multiprocess import Lock, Manager
+    filename_base = "obst-" + str(obst.id)
+    # Create all requested directories if they don't exist yet
+    Path(os.path.join(output_dir, filename_base + "-data")).mkdir(parents=True, exist_ok=True)
+
+    meta = {"BoundingBox": obst.bounding_box.as_list(), "QuantityNum": len(obst.quantities)}
+    m = Manager()
+    lock = m.Lock()
+    meta["Quantities"] = m.list()
+
+    def worker(quantity, bndf_data):
+        quantity_name = quantity.name.replace(" ", "_").replace(".", "-")
+        filename = filename_base + "_quantity-" + quantity_name + ".dat"
+
+        out = {"Quantity": quantity.name.replace(" ", "_").replace(".", "-"), "DataValMax": -100000.,
+               "DataValMin": 100000., "ScaleFactor": 1, "DataFile": os.path.join(filename_base + "-data", filename),
+               "Orientations": list()}
+        for bndf in bndf_data:
+            out["DataValMax"] = max(out["DataValMax"], np.max(bndf.upper_bounds))
+            out["DataValMin"] = min(out["DataValMin"], np.min(bndf.lower_bounds))
+        out["DataValMax"] = float(out["DataValMax"])
+        out["DataValMin"] = float(out["DataValMin"])
+        out["ScaleFactor"] = 255.0 / out["DataValMax"]
+
+        # Abort if no useful data is available
+        if meta[quantity]["DataValMax"] <= 0:
+            return
+
+        with open(os.path.join(output_dir, quantity_name, filename_base + "-data", filename), 'wb') as rawfile:
+            orientations = set()
+            for orientation in (-3, -2, -1, 1, 2, 3):
+                patches = list()
+                for bndf in bndf_data:
+                    if orientation in bndf.data:
+                        orientations.add(orientation)
+                        patches.append(bndf.data[orientation])
+
+                if len(patches) == 0:
+                    continue
+
+                # Combine patches to a single face for plotting
+                patches = sort_patches_cartesian(patches)
+
+                shape_dim1 = sum([patch_row[0].shape[0] for patch_row in patches])
+                shape_dim2 = sum([patch.shape[1] for patch in patches[0]])
+                n_t = patches[0][0].n_t  # Number of timesteps
+
+                face = np.empty(shape=(n_t, shape_dim1, shape_dim2))
+                dim1_pos = 0
+                dim2_pos = 0
+                for patch_row in patches:
+                    d1 = patch_row[0].shape[0]
+                    for patch in patch_row:
+                        d2 = patch.shape[1]
+                        face[:, dim1_pos:dim1_pos + d1, dim2_pos:dim2_pos + d2] = patch.data
+                        dim2_pos += d2
+                    dim1_pos += d1
+                    dim2_pos = 0
+
+                face = (face * meta["ScaleFactor"]).astype(np.uint8)
+
+                if abs(orientation) == 1:
+                    spacing1 = (meta["BoundingBox"][3] - meta["BoundingBox"][2]) / face.shape[1]
+                    spacing2 = (meta["BoundingBox"][5] - meta["BoundingBox"][4]) / face.shape[2]
+                elif abs(orientation) == 2:
+                    spacing1 = (meta["BoundingBox"][1] - meta["BoundingBox"][0]) / face.shape[0]
+                    spacing2 = (meta["BoundingBox"][5] - meta["BoundingBox"][4]) / face.shape[2]
+                else:
+                    spacing1 = (meta["BoundingBox"][1] - meta["BoundingBox"][0]) / face.shape[0]
+                    spacing2 = (meta["BoundingBox"][3] - meta["BoundingBox"][2]) / face.shape[1]
+
+
+                out["Orientations"].append({
+                    "Orientation": orientation,
+                    "MeshPos": f"{meta['BoundingBox'][0]:.6} {meta['BoundingBox'][2]:.6} {meta['BoundingBox'][4]:.6}",
+                    "Spacing": f"{bndf_data[0].times[1] - bndf_data[0].times[0]:.6} {spacing1:.6} {spacing2:.6}",
+                    "DimSize": f"{face.shape[2]} {face.shape[1]} {face.shape[2]}"
+                })
+
+                for d in face[:, [2, 0, 1]]:  # Make time the first dimension so we can easily iterate over it
+                    if ordering == 'F':
+                        d = d.T
+                    d.tofile(rawfile)
+
+            out["NumOrientations"] = len(orientations)
+
+        with lock:
+            meta["Quantities"].append(out)
+
+    worker_args = list()
+    for i, quantity in enumerate(obst.quantities):
+        bndf_data = obst.get_boundary_data(quantity)
+        worker_args.append((quantity, bndf_data))
+    Pool(8).map(lambda args: worker(*args), worker_args)
+
+    meta["Quantities"] = list(meta["Quantities"])
+
+    with open(os.path.join(output_dir, filename_base + ".yaml"), 'w') as metafile:
+        import yaml
+    yaml.dump(meta, metafile)

fdsreader-1.3.7/fdsreader/export/slcf_exporter.py

@@ -0,0 +1,63 @@
+import os
+from pathlib import Path
+import numpy as np
+from typing_extensions import Literal
+from ..slcf import Slice
+
+
+def export_slcf_raw(slc: Slice, output_dir: str, ordering: Literal['C', 'F'] = 'C'):
+    """Exports the 3d arrays to raw binary files with corresponding .yaml meta files.
+
+    :param slc: The :class:`Slice` object to export.
+    :param output_dir: The directory in which to save all files.
+    :param ordering: Whether to write the data in C or Fortran ordering.
+    """
+    from pathos.pools import ProcessPool as Pool
+    from multiprocess import Lock, Manager
+    slc2d = slc.type == '2D'
+    meta = {"DataValMax": float(slc.vmax), "DataValMin": float(slc.vmin), "ScaleFactor": 255. / (float(slc.vmax) - float(slc.vmin)),
+            "MeshNum": len(slc.subslices), "Quantity": slc.quantity.name}
+
+    filename_base = ("slice" + ("2D-" if slc2d else "3D-") + slc.id.lower()).replace(" ", "_").replace(".", "-")
+    # Create all requested directories if they don't exist yet
+    Path(os.path.join(output_dir, filename_base + "-data")).mkdir(parents=True, exist_ok=True)
+
+    m = Manager()
+    meta["Meshes"] = m.list()
+    lock = m.Lock()
+
+    def worker(mesh, subslice):
+        mesh_id = mesh.id.replace(" ", "_").replace(".", "-")
+        filename = filename_base + "_mesh-" + mesh_id + ".dat"
+
+        data = ((subslice.data - meta["DataValMin"]) * meta["ScaleFactor"]).astype(np.uint8)
+        shape = data.shape
+        if slc2d:
+            shape = shape[:subslice.orientation] + (1,) + shape[subslice.orientation:]
+
+        with open(os.path.join(output_dir, filename_base + "-data", filename), 'wb') as rawfile:
+            for d in data:
+                if ordering == 'F':
+                    d = d.T
+                d.tofile(rawfile)
+
+        spacing = [slc.times[1] - slc.times[0],
+                   mesh.coordinates['x'][1] - mesh.coordinates['x'][0],
+                   mesh.coordinates['y'][1] - mesh.coordinates['y'][0],
+                   mesh.coordinates['z'][1] - mesh.coordinates['z'][0]]
+        with lock:
+            meta["Meshes"].append({
+                "Mesh": mesh_id,
+                "DataFile": os.path.join(filename_base + "-data", filename),
+                "MeshPos": f"{mesh.coordinates['x'][0]:.6} {mesh.coordinates['y'][0]:.6} {mesh.coordinates['z'][0]:.6}",
+                "Spacing": f"{spacing[0]:.6} {spacing[1]:.6} {spacing[2]:.6} {spacing[3]:.6}",
+                "DimSize": f"{shape[0]} {shape[1]} {shape[2]} {shape[3]}"
+            })
+
+    Pool(8).map(lambda args: worker(*args), list(slc._subslices.items()))
+
+    meta["Meshes"] = list(meta["Meshes"])
+
+    with open(os.path.join(output_dir, filename_base + ".yaml"), 'w') as metafile:
+        import yaml
+        yaml.dump(meta, metafile)

fdsreader-1.3.7/fdsreader/export/smoke3d_exporter.py

@@ -0,0 +1,70 @@
+import os
+from pathlib import Path
+import numpy as np
+from typing_extensions import Literal
+from ..smoke3d import Smoke3D
+
+
+def export_smoke_raw(smoke3d: Smoke3D, output_dir: str, ordering: Literal['C', 'F'] = 'C'):
+    """Exports the 3d arrays to raw binary files with corresponding .yaml meta files.
+
+    :param smoke3d: The :class:`Smoke3D` object to export.
+    :param output_dir: The directory in which to save all files.
+    :param ordering: Whether to write the data in C or Fortran ordering.
+    """
+    from pathos.pools import ProcessPool as Pool
+    from multiprocess import Lock, Manager
+    filename_base = ("smoke-" + smoke3d.quantity.name.lower()).replace(" ", "_").replace(".", "-")
+    # Create all requested directories if they don't exist yet
+    Path(os.path.join(output_dir, filename_base + "-data")).mkdir(parents=True, exist_ok=True)
+
+    meta = {"DataValMax": -100000., "DataValMin": 100000., "ScaleFactor": 1, "MeshNum": len(smoke3d.subsmokes),
+            "Quantity": smoke3d.quantity.name}
+
+    for subsmoke in smoke3d._subsmokes.values():
+        meta["DataValMax"] = max(meta["DataValMax"], np.max(subsmoke.data))
+        meta["DataValMin"] = min(meta["DataValMin"], np.min(subsmoke.data))
+    meta["DataValMax"] = float(meta["DataValMax"])
+    meta["DataValMin"] = float(meta["DataValMin"])
+    meta["ScaleFactor"] = 255.0 / meta["DataValMax"]
+
+    # Abort if no useful data is available
+    if meta["DataValMax"] <= 0:
+        return
+
+    m = Manager()
+    meta["Meshes"] = m.list()
+    lock = m.Lock()
+
+    def worker(mesh, subsmoke):
+        mesh_id = mesh.id.replace(" ", "_").replace(".", "-")
+        filename = filename_base + "_mesh-" + mesh_id + ".dat"
+
+        data = (subsmoke.data * meta["ScaleFactor"]).astype(np.uint8)
+
+        with open(os.path.join(output_dir, filename_base + "-data", filename), 'wb') as rawfile:
+            for d in data:
+                if ordering == 'F':
+                    d = d.T
+                d.tofile(rawfile)
+
+        spacing = [smoke3d.times[1] - smoke3d.times[0],
+                   mesh.coordinates['x'][1] - mesh.coordinates['x'][0],
+                   mesh.coordinates['y'][1] - mesh.coordinates['y'][0],
+                   mesh.coordinates['z'][1] - mesh.coordinates['z'][0]]
+        with lock:
+            meta["Meshes"].append({
+                "Mesh": mesh_id,
+                "DataFile": os.path.join(filename_base + "-data", filename),
+                "MeshPos": f"{mesh.coordinates['x'][0]:.6} {mesh.coordinates['y'][0]:.6} {mesh.coordinates['z'][0]:.6}",
+                "Spacing": f"{spacing[0]:.6} {spacing[1]:.6} {spacing[2]:.6} {spacing[3]:.6}",
+                "DimSize": f"{data.shape[0]} {data.shape[1]} {data.shape[2]} {data.shape[3]}"
+            })
+
+    Pool(8).map(lambda args: worker(*args), list(smoke3d._subsmokes.items()))
+
+    meta["Meshes"] = list(meta["Meshes"])
+
+    with open(os.path.join(output_dir, filename_base + ".yaml"), 'w') as metafile:
+        import yaml
+        yaml.dump(meta, metafile)

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/fds_classes/mesh.py

@@ -68,7 +68,7 @@ class Mesh:
             as obstructions may be hidden as specific points in time.
         """
         orientation = subslice.orientation
-        value = subslice.extent[orientation - 1][0]
+        value = subslice.extent[orientation][0]
         cell_centered = subslice.cell_centered
 
         slc_index = self.coordinate_to_index((value,), dimension=(orientation,), cell_centered=cell_centered)[0]
@@ -87,6 +87,7 @@ class Mesh:
         :param coordinate: Tuple of 3 floats. If the dimension parameter is supplied, up to 2
             dimensions can be left out from the tuple.
         :param dimension: The dimensions in which to return the indices (1=x, 2=y, 3=z).
+        :param cell_centered: Instead of finding the nearest point on the mesh, find the center of the nearest cell.
         """
         # Convert possible integer input to chars
         dimension = tuple(('x', 'y', 'z')[dim - 1] if type(dim) == int else dim for dim in dimension)
@@ -105,6 +106,25 @@ class Mesh:
                 ret.append(idx)
         return tuple(ret)
 
+    def get_nearest_coordinate(self, coordinate: Tuple[float, ...],
+                            dimension: Tuple[Literal[1, 2, 3, 'x', 'y', 'z'], ...] = ('x', 'y', 'z'),
+                            cell_centered=False) -> Tuple[float, ...]:
+        """Finds the nearest point in the mesh's grid.
+
+        :param coordinate: Tuple of 3 floats. If the dimension parameter is supplied, up to 2
+            dimensions can be left out from the tuple.
+        :param dimension: The dimensions in which to return the indices (1=x, 2=y, 3=z).
+        :param cell_centered: Instead of finding the nearest point on the mesh, find the center of the nearest cell.
+        """
+        indices = self.coordinate_to_index(coordinate, dimension, cell_centered)
+        ret = list()
+        for i, dim in enumerate(dimension):
+            coords = self.coordinates[dim]
+            if cell_centered:
+                coords = coords[:-1] + (coords[1] - coords[0]) / 2
+            ret.append(coords[indices[i]])
+        return tuple(ret)
+
     def _add_patches(self, bid: int, cell_centered: bool, quantity: str, short_name: str, unit: str,
                      patches: List[Patch], times: np.ndarray, n_t: int, lower_bounds: np.ndarray,
                      upper_bounds: np.ndarray):

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/pl3d/pl3d.py

@@ -88,6 +88,12 @@ class Plot3D(np.lib.mixins.NDArrayOperatorsMixin):
         """
         return self._subplots[mesh]
 
+    def get_quantity_index(self, quantity: str):
+        """Returns the index of the quantity for the fourth dimension of the data array.
+        """
+        return next(i for i, q in enumerate(self.quantities) if
+                    q.name.lower() == quantity.lower() or q.short_name.lower() == quantity.lower())
+
     @implements(np.mean)
     def mean(self) -> np.ndarray:
         """Calculates the mean for each quantity individually of the whole Plot3D.

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/simulation.py

@@ -43,8 +43,8 @@ class Simulation:
     :ivar isosurfaces: All defined isosurfaces combined into a :class:`IsosurfaceCollection`.
     :ivar particles: All defined particles combined into a :class:`ParticleCollection`.
     :ivar evacs: All defined evacuations combined into a :class:`EvacCollection`.
-    :ivar devices: List containing all :class:`Device`s defined in this simulation.
-    :ivar profiles: Dictionary mapping profile ids to the corresponding :class:`Profile`s defined in this simulation.
+    :ivar devices: List containing all :class:`Device` s defined in this simulation.
+    :ivar profiles: Dictionary mapping profile ids to the corresponding :class:`Profile` s defined in this simulation.
     :ivar geoms: List containing all geometries (:class:`Geometry`) defined in this simulation.
     :ivar geom_data: All geometry data by quantity combined into a :class:`GeometryCollection`.
     :ivar cpu: Dictionary mapping .csv header keys to numpy arrays containing cpu data.
@@ -924,7 +924,7 @@ class Simulation:
     def _load_DEVC_data(self, file_path: str):
         with open(file_path, 'r') as infile:
             units = infile.readline().split(',')
-            names = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',')]
+            names = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',"')]
             values = np.genfromtxt(infile, delimiter=',', dtype=np.float32, autostrip=True)
             for k in range(len(names)):
                 devc = self.devices[names[k]]
@@ -938,7 +938,7 @@ class Simulation:
         if os.path.exists(line_path):
             with open(line_path, 'r') as infile:
                 units = infile.readline()
-                names = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',')]
+                names = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',"')]
                 data = np.genfromtxt(infile, delimiter=',', dtype=np.float32, autostrip=True)
                 for k, key in enumerate(names):
                     if key in self.devices:
@@ -953,7 +953,7 @@ class Simulation:
     def _load_HRR_data(self, file_path: str) -> Dict[str, np.ndarray]:
         with open(file_path, 'r') as infile:
             infile.readline()
-            keys = infile.readline().split(',')
+            keys = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',')]
             values = np.genfromtxt(infile, delimiter=',', dtype=np.float32, autostrip=True)
             return self._transform_csv_data(keys, values, [np.float32] * len(keys))
 
@@ -961,7 +961,7 @@ class Simulation:
     def _load_step_data(self, file_path: str) -> Dict[str, np.ndarray]:
         with open(file_path, 'r') as infile:
             infile.readline()
-            keys = infile.readline().split(',')
+            keys = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',')]
             dtypes = [np.float32] * len(keys)
             dtypes[0] = int
             dtypes[1] = np.dtype("datetime64[ms]")
@@ -973,7 +973,7 @@ class Simulation:
         file_path = os.path.join(self.root_path, self.chid + "_cpu.csv")
         if os.path.exists(file_path):
             with open(file_path, 'r') as infile:
-                keys = infile.readline().split(",")
+                keys = [name.replace('"', '').replace('\n', '').strip() for name in infile.readline().split(',')]
                 dtypes = [np.float32] * len(keys)
                 dtypes[0] = int
                 values = np.genfromtxt(infile, delimiter=',', dtype=dtypes, autostrip=True)

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/slcf/SliceCollection.py

@@ -16,7 +16,7 @@ class SliceCollection(FDSDataCollection):
 
     @property
     def quantities(self) -> List[Quantity]:
-        return list({slc.name for slc in self})
+        return list({slc.quantity.name for slc in self})
 
     def filter_by_quantity(self, quantity: Union[str, Quantity]):
         """Filters all slices by a specific quantity.

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/slcf/slice.py

@@ -58,7 +58,7 @@ class SubSlice:
         return shape
 
     @property
-    def orientation(self) -> Literal[1, 2, 3]:
+    def orientation(self) -> Literal[0, 1, 2, 3]:
         """Orientation [1,2,3] of the slice in case it is 2D, 0 otherwise.
         """
         return self._parent_slice.orientation
@@ -147,7 +147,7 @@ class Slice(np.lib.mixins.NDArrayOperatorsMixin):
     """Slice file data container including metadata. Consists of multiple subslices, one for each
         mesh the slice cuts through. In case a slice cuts right through the border of two meshes, the generated data
         would be duplicated. For edge-centered slices a random of both generated slices will be discarded as the data
-        is completely identical. For cell-centered slices the data of both slices will be saved as :class:`SubSlice`s,
+        is completely identical. For cell-centered slices the data of both slices will be saved as :class:`SubSlice` s,
         therefore it might seem as if all slices would be duplicated, in reality however the slices might contain
         different data.
 
@@ -258,8 +258,7 @@ class Slice(np.lib.mixins.NDArrayOperatorsMixin):
         return list(self._subslices.values())
 
     @property
-    def extent_dirs(self) -> Tuple[
-        Literal['x', 'y', 'z'], Literal['x', 'y', 'z'], Literal['x', 'y', 'z']]:
+    def extent_dirs(self) -> Tuple[Literal['x', 'y', 'z'], Literal['x', 'y', 'z'], Literal['x', 'y', 'z']]:
         """The directions in which there is an extent. All three dimensions in case the slice is 3D.
         """
         ior = self.orientation
@@ -333,8 +332,67 @@ class Slice(np.lib.mixins.NDArrayOperatorsMixin):
         for subslice in self._subslices.values():
             subslice.clear_cache()
 
+    def get_2d_slice_from_3d(self, slice_direction: Literal['x', 'y', 'z', 1, 2, 3], value: float):
+        """Creates a 2D-Slice from a 3D-Slice by slicing the Slice.
+        :param slice_direction: The direction in which to cut through the slice.
+        :param value: The position at which to start cutting through the slice.
+        """
+        if type(slice_direction) == str:
+            slice_dim = {'x': 1, 'y': 2, 'z': 3}[slice_direction]
+        else:
+            slice_dim = slice_direction
+            slice_direction = ('x', 'y', 'z')[slice_dim - 1]
+        new_slice = deepcopy(self)
+
+        to_remove = list()
+        for mesh in new_slice._subslices.keys():
+            subslc = new_slice._subslices[mesh]
+            # Check if the new slice cuts through the subslice
+            cut_index = mesh.coordinate_to_index((value,), (slice_direction,),
+                                                 cell_centered=self.cell_centered)
+            cut_value = mesh.get_nearest_coordinate((value,), (slice_direction,),
+                                                    cell_centered=self.cell_centered)[0]
+            if mesh.coordinates[slice_direction][0] <= value <= mesh.coordinates[slice_direction][-1] and subslc.extent[slice_dim - 1][0] <= cut_value <= subslc.extent[slice_dim - 1][1]:
+                shape = subslc.dimension.shape(cell_centered=self.cell_centered)
+                indices = [slice(subslc.n_t)]
+
+                if subslc.dimension.x == 1 or subslc.dimension.y == 1 or subslc.dimension.z == 1:
+                    indices.extend((slice(shape[0]), slice(shape[1])))
+                else:
+                    indices.extend((slice(shape[0]), slice(shape[1]), slice(shape[2])))
+                    indices[slice_dim - 1] = slice(cut_index[0], cut_index[0] + 1, 1)
+
+                subslc._data = subslc.data[tuple(indices)]
+                for direction in subslc.vector_filenames.keys():
+                    subslc._vector_data[direction] = subslc.vector_data[direction][tuple(indices)]
+                subslc.extent._extents[slice_dim - 1] = (0, 0)
+            else:
+                to_remove.append(mesh)
+
+        for mesh in to_remove:
+            del new_slice._subslices[mesh]
+
+        vals = new_slice._subslices.values()
+        new_slice.extent = Extent(min(vals, key=lambda e: e.extent.x_start).extent.x_start,
+                                  max(vals, key=lambda e: e.extent.x_end).extent.x_end,
+                                  min(vals, key=lambda e: e.extent.y_start).extent.y_start,
+                                  max(vals, key=lambda e: e.extent.y_end).extent.y_end,
+                                  min(vals, key=lambda e: e.extent.z_start).extent.z_start,
+                                  max(vals, key=lambda e: e.extent.z_end).extent.z_end)
+
+        if new_slice.extent.x_start == new_slice.extent.x_end:
+            new_slice.orientation = 1
+        elif new_slice.extent.y_start == new_slice.extent.y_end:
+            new_slice.orientation = 2
+        elif new_slice.extent.z_start == new_slice.extent.z_end:
+            new_slice.orientation = 3
+        else:
+            new_slice.orientation = 0
+
+        return new_slice
+
     def sort_subslices_cartesian(self):
-        """Returns all subslices sorted in cartesian coordinates (2D-slices only).
+        """Returns all subslices sorted in cartesian coordinates.
         """
         slices = list(self._subslices.values())
         slices_cart = [[slices[0]]]
@@ -403,6 +461,9 @@ class Slice(np.lib.mixins.NDArrayOperatorsMixin):
         return slc_array
 
     def to_global_nonuniform(self) -> np.ndarray:
+        """Creates a global 2D-numpy ndarray from all subslices (2D-slices only).
+            Beware, this method might create sparse np-arrays that consume lots of memory.
+        """
         # The global grid will use the finest mesh as base and duplicate values of the coarser meshes
         # Therefore we first find the finest mesh and calculate the step size in each dimension
         coords = self.coordinates
@@ -437,7 +498,7 @@ class Slice(np.lib.mixins.NDArrayOperatorsMixin):
                 end_idx[dim] = int((mesh.coordinates[dim][-1] - start_coordinates[dim]) / step_sizes[dim]) + n_repeat
 
                 if n_repeat > 1:
-                    slc_data = np.repeat(slc_data, n_repeat, axis=axis+1)
+                    slc_data = np.repeat(slc_data, n_repeat, axis=axis + 1)
 
             grid[:, start_idx['x']: end_idx['x'], start_idx['y']: end_idx['y'],
             start_idx['z']: end_idx['z']] = slc_data.reshape(

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/smoke3d/Smoke3DCollection.py

@@ -6,7 +6,7 @@ from fdsreader.utils.data import FDSDataCollection, Quantity
 
 class Smoke3DCollection(FDSDataCollection):
     """Collection of :class:`Smoke3D` objects. Offers extensive functionality for filtering and
-        using Smoke3Ds as well as its subclasses such as :class:`SubSmoke3D`.
+        using Smoke3Ds as well as its subclasses such as :class:`SubSmoke3D` .
     """
 
     def __init__(self, *smoke3ds: Iterable[Smoke3D]):

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/smoke3d/smoke3d.py

@@ -52,7 +52,7 @@ class SubSmoke3D:
                 nx, ny, nz = int(header[3]), int(header[5]), int(header[7])
                 data_shape = (nx + 1, ny + 1, nz + 1)
 
-                self._data = np.empty((self.times.size,) + data_shape)
+                self._data = np.empty((self.times.size,) + data_shape, dtype=np.float32)
 
                 for t in range(self.times.size):
                     fdtype.read(infile, fdtype.FLOAT, 1)  # Skip time value
@@ -127,54 +127,9 @@ class Smoke3D(np.lib.mixins.NDArrayOperatorsMixin):
         """
         return self._subsmokes[mesh]
 
-    def export_raw(self, output_dir: str, bytesize: int, ordering: Literal['C', 'F'] = 'C'):
-        """Exports the 3d arrays to raw binary files with corresponding .yaml meta files.
-
-        :param output_dir: The directory in which to save all files.
-        :param bytesize: The number of bytes used to save the data.
-        :param ordering: Whether to write the data in C or Fortran ordering.
-        """
-        if bytesize == 1:
-            dtype = np.uint8
-            dtype_str = "uchar"
-        elif bytesize == 2:
-            dtype = np.uint16
-            dtype_str = "ushort"
-        else:
-            dtype = np.uint32
-            dtype_str = "uint"
-
-        meta = {"DataType": dtype_str, "Meshes": str(len(self._subsmokes)), "MeshData": list()}
-
-        filename_base = "smoke-" + self.quantity.name.lower()
-        for mesh, subsmoke in self._subsmokes.items():
-            filename = filename_base + "_mesh-" + mesh.id
-            filename = filename.replace(" ", "_").replace(".", "-")
-            filename += ".dat"
-
-            data = subsmoke.data.astype(dtype)
-
-            with open(os.path.join(output_dir, filename), 'wb') as rawfile:
-                for d in data:
-                    if ordering == 'F':
-                        d = d.T
-                    d.tofile(rawfile)
-
-            spacing = [self.times[1] - self.times[0],
-                       mesh.coordinates['x'][1] - mesh.coordinates['x'][0],
-                       mesh.coordinates['y'][1] - mesh.coordinates['y'][0],
-                       mesh.coordinates['z'][1] - mesh.coordinates['z'][0]]
-            meta["MeshData"].append({
-                "Mesh": mesh.id.replace(" ", "_").replace(".", "-"),
-                "DataFile": filename,
-                "MeshPos": f"{mesh.coordinates['x'][0]:.6} {mesh.coordinates['y'][0]:.6} {mesh.coordinates['z'][0]:.6}",
-                "Spacing": f"{spacing[0]:.6} {spacing[1]:.6} {spacing[2]:.6} {spacing[3]:.6}",
-                "DimSize": f"{subsmoke.data.shape[0]} {subsmoke.data.shape[1]} {subsmoke.data.shape[2]} {subsmoke.data.shape[3]}"
-            })
-
-        import yaml
-        with open(os.path.join(output_dir, filename_base + ".yaml"), 'w') as metafile:
-            yaml.dump(meta, metafile)
+    @property
+    def subsmokes(self):
+        return self._subsmokes.items()
 
     @property
     def vmax(self):

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader/utils/extent.py

@@ -30,14 +30,14 @@ class Extent:
                                                                                        self.y_start, self.y_end,
                                                                                        self.z_start, self.z_end)
 
-    def __getitem__(self, item: Union[int, Literal['x', 'y', 'z']]):
+    def __getitem__(self, item: Union[Literal['x', 'y', 'z', 1, 2, 3]]):
         if item == 'x':
             return self.x_start, self.x_end
         elif item == 'y':
             return self.y_start, self.y_end
         elif item == 'z':
             return self.z_start, self.z_end
-        return self._extents[item]
+        return self._extents[item - 1]
 
     @property
     def x_start(self):

{fdsreader-1.2.8 → fdsreader-1.3.7/fdsreader.egg-info}/PKG-INFO

@@ -1,8 +1,8 @@
 Metadata-Version: 2.1
 Name: fdsreader
-Version: 1.2.8
+Version: 1.3.7
 Summary: Python reader for data generated by FDS.
-Home-page: https://github.com/JanVogelsang/fdsreader
+Home-page: https://github.com/FireDynamics/fdsreader
 Author: FZJ IAS-7 (Prof. Dr. Lukas Arnold, Jan Vogelsang)
 Author-email: j.vogelsang@fz-juelich.de
 License: UNKNOWN

{fdsreader-1.2.8 → fdsreader-1.3.7}/fdsreader.egg-info/SOURCES.txt

@@ -19,6 +19,10 @@ fdsreader/bndf/utils.py
 fdsreader/evac/EvacCollection.py
 fdsreader/evac/__init__.py
 fdsreader/evac/evacuation.py
+fdsreader/export/__init__.py
+fdsreader/export/obst_exporter.py
+fdsreader/export/slcf_exporter.py
+fdsreader/export/smoke3d_exporter.py
 fdsreader/fds_classes/MeshCollection.py
 fdsreader/fds_classes/__init__.py
 fdsreader/fds_classes/mesh.py

fdsreader-1.3.7/requirements.txt

@@ -0,0 +1,118 @@
+alabaster~=0.7.12
+appdirs~=1.4.4
+argon2-cffi~=20.1.0
+async-generator~=1.10
+attrs~=20.3.0
+autodocsumm~=0.2.2
+Automat~=20.2.0
+Babel~=2.9.0
+backcall~=0.2.0
+bcrypt~=3.2.0
+bleach~=3.3.0
+brotlipy~=0.7.0
+certifi~=2020.12.5
+cffi~=1.14.5
+chardet~=4.0.0
+click~=7.1.2
+colorama~=0.4.4
+constantly~=15.1.0
+cryptography~=3.4.7
+cycler~=0.10.0
+decorator~=5.0.6
+defusedxml~=0.7.1
+docutils~=0.16
+entrypoints~=0.3
+environment-kernels~=1.1.1
+hyperlink~=21.0.0
+idna~=2.10
+imageio~=2.9.0
+imageio-ffmpeg~=0.4.3
+imagesize~=1.2.0
+importlib-metadata~=3.10.0
+incremental~=21.3.0
+ipykernel~=5.3.4
+ipython~=7.22.0
+ipython-genutils~=0.2.0
+jedi~=0.17.0
+Jinja2~=2.11.3
+jsonschema~=3.2.0
+jupyter-client~=6.1.12
+jupyter-core~=4.7.1
+jupyterlab-pygments~=0.1.2
+kiwisolver~=1.3.1
+MarkupSafe~=1.1.1
+matplotlib~=3.4.1
+meshio~=4.3.13
+mistune~=0.8.4
+mkl-fft~=1.3.0
+mkl-random~=1.1.1
+mkl-service~=2.3.0
+nbclient~=0.5.3
+nbconvert~=6.0.7
+nbformat~=5.1.3
+nbsphinx~=0.8.3
+nest-asyncio~=1.5.1
+notebook~=6.3.0
+numpy~=1.20.2
+olefile~=0.46
+packaging~=20.9
+pandocfilters~=1.4.3
+parso~=0.8.2
+pickleshare~=0.7.5
+Pillow~=8.2.0
+pip~=21.0.1
+prometheus-client~=0.10.1
+prompt-toolkit~=3.0.17
+pyasn1~=0.4.8
+pyasn1-modules~=0.2.8
+pycparser~=2.20
+Pygments~=2.8.1
+PyHamcrest~=2.0.2
+pyOpenSSL~=20.0.1
+pyparsing~=2.4.7
+pyrsistent~=0.17.3
+PySocks~=1.7.1
+python-dateutil~=2.8.1
+pytz~=2021.1
+pyvista~=0.29.1
+pywin32~=227
+pywinpty~=0.5.7
+pyzmq~=20.0.0
+requests~=2.25.1
+rise~=5.7.1
+scooby~=0.5.7
+Send2Trash~=1.5.0
+service-identity~=18.1.0
+setuptools~=58.0.0
+six~=1.15.0
+snowballstemmer~=2.1.0
+Sphinx~=3.5.4
+sphinx-rtd-theme~=0.5.2
+sphinxcontrib-applehelp~=1.0.2
+sphinxcontrib-devhelp~=1.0.2
+sphinxcontrib-htmlhelp~=1.0.3
+sphinxcontrib-jsmath~=1.0.1
+sphinxcontrib-qthelp~=1.0.3
+sphinxcontrib-serializinghtml~=1.1.4
+terminado~=0.9.4
+testpath~=0.4.4
+tornado~=6.1
+traitlets~=5.0.5
+transforms3d~=0.3.1
+Twisted~=21.2.0
+twisted-iocpsupport~=1.0.1
+typing-extensions~=3.7.4.3
+urllib3~=1.26.4
+vtk~=9.0.1
+wcwidth~=0.2.5
+webencodings~=0.5.1
+wheel~=0.36.2
+win-inet-pton~=1.1.0
+wincertstore~=0.2
+pyyaml~=5.4.1
+zipp~=3.4.1
+zope.interface~=5.3.0
+pyvistaqt~=0.4.0
+typing_extensions~=3.7.4.3
+pathos~=0.2.8
+multiprocess~=0.70.12.2

{fdsreader-1.2.8 → fdsreader-1.3.7}/setup.py

@@ -4,7 +4,7 @@ import setuptools
 
 base_dir = os.path.dirname(os.path.realpath(__file__))
 
-with open(os.path.join(base_dir, "README.md"), 'r') as f:
+with open(os.path.join(base_dir, "README.md"), 'r', encoding="utf-8") as f:
     long_description = f.read()
 
 setuptools.setup(
@@ -16,7 +16,7 @@ setuptools.setup(
     description="Python reader for data generated by FDS.",
     long_description=long_description,
     long_description_content_type="text/markdown",
-    url="https://github.com/JanVogelsang/fdsreader",
+    url="https://github.com/FireDynamics/fdsreader",
     packages=setuptools.find_packages(),
     classifiers=[
         "Programming Language :: Python :: 3",

fdsreader-1.2.8/requirements.txt

@@ -1,113 +0,0 @@
-alabaster==0.7.12
-appdirs==1.4.4
-argon2-cffi==20.1.0
-async-generator==1.10
-attrs==20.3.0
-autodocsumm==0.2.2
-Automat==20.2.0
-Babel==2.9.0
-backcall==0.2.0
-bcrypt==3.2.0
-bleach==3.3.0
-brotlipy==0.7.0
-certifi==2020.12.5
-cffi==1.14.5
-chardet==4.0.0
-click==7.1.2
-colorama==0.4.4
-constantly==15.1.0
-cryptography==3.4.7
-cycler==0.10.0
-decorator==5.0.6
-defusedxml==0.7.1
-docutils==0.16
-entrypoints==0.3
-environment-kernels==1.1.1
-hyperlink==21.0.0
-idna==2.10
-imageio==2.9.0
-imageio-ffmpeg==0.4.3
-imagesize==1.2.0
-importlib-metadata==3.10.0
-incremental==21.3.0
-ipykernel==5.3.4
-ipython==7.22.0
-ipython-genutils==0.2.0
-jedi==0.17.0
-Jinja2==2.11.3
-jsonschema==3.2.0
-jupyter-client==6.1.12
-jupyter-core==4.7.1
-jupyterlab-pygments==0.1.2
-kiwisolver==1.3.1
-MarkupSafe==1.1.1
-matplotlib==3.4.1
-meshio==4.3.13
-mistune==0.8.4
-mkl-fft==1.3.0
-mkl-random==1.1.1
-mkl-service==2.3.0
-nbclient==0.5.3
-nbconvert==6.0.7
-nbformat==5.1.3
-nbsphinx==0.8.3
-nest-asyncio==1.5.1
-notebook==6.3.0
-numpy==1.20.2
-olefile==0.46
-packaging==20.9
-pandocfilters==1.4.3
-parso==0.8.2
-pickleshare==0.7.5
-Pillow==8.2.0
-pip==21.0.1
-prometheus-client==0.10.1
-prompt-toolkit==3.0.17
-pyasn1==0.4.8
-pyasn1-modules==0.2.8
-pycparser==2.20
-Pygments==2.8.1
-PyHamcrest==2.0.2
-pyOpenSSL==20.0.1
-pyparsing==2.4.7
-pyrsistent==0.17.3
-PySocks==1.7.1
-python-dateutil==2.8.1
-pytz==2021.1
-pyvista==0.29.1
-pywin32==227
-pywinpty==0.5.7
-pyzmq==20.0.0
-requests==2.25.1
-rise==5.7.1
-scooby==0.5.7
-Send2Trash==1.5.0
-service-identity==18.1.0
-setuptools==52.0.0.post20210125
-six==1.15.0
-snowballstemmer==2.1.0
-Sphinx==3.5.4
-sphinx-rtd-theme==0.5.2
-sphinxcontrib-applehelp==1.0.2
-sphinxcontrib-devhelp==1.0.2
-sphinxcontrib-htmlhelp==1.0.3
-sphinxcontrib-jsmath==1.0.1
-sphinxcontrib-qthelp==1.0.3
-sphinxcontrib-serializinghtml==1.1.4
-terminado==0.9.4
-testpath==0.4.4
-tornado==6.1
-traitlets==5.0.5
-transforms3d==0.3.1
-Twisted==21.2.0
-twisted-iocpsupport==1.0.1
-typing-extensions==3.7.4.3
-urllib3==1.26.4
-vtk==9.0.1
-wcwidth==0.2.5
-webencodings==0.5.1
-wheel==0.36.2
-win-inet-pton==1.1.0
-wincertstore==0.2
-zipp==3.4.1
-zope.interface==5.3.0