Merge branch 'HelgeGehring:master' into new_spiral

Author: fbeutel

CHANGELOG.md

@@ -1,10 +1,17 @@
 Changelog
 =========
 
-Unreleased
+1.2.0
 ----------
+* Added meep integration
+* GDSII-export: Added support for LineStrings
+
+1.1.4
+-----
 * Waveguide: added add_left_bend and add_right_bend to make code easier readable
 * added alphanumeric_to_id as an inverse of id_to_alphanumeric
+* allow to limit the numbers of workers for parallel export
+* fixed oasis export
 
 1.1.3
 -----

README.md

@@ -56,6 +56,10 @@ The structures are organized in cells, which allow:
 * Automatized generation of region layers
 * Parallelized export
 
+Additionally the structures can conveniently be simulated by:
+
+* Using the meep integration (FDTD)
+
 Finally, there are also different formats in which the pattern can be exported:
 
 * The GDSII-format, which is quite often used for (electron beam/...)-lithography

docs/changelog/changelog.rst

@@ -0,0 +1 @@
+.. include:: ../../CHANGELOG.md

docs/conf.py

@@ -20,6 +20,7 @@
     'sphinx.ext.imgmath',
     'matplotlib.sphinxext.plot_directive',
     'sphinx.ext.graphviz',
+    'm2r2'
 ]
 
 plot_rcparams = {'savefig.bbox': 'tight'}

docs/index.rst

@@ -123,6 +123,7 @@ _________________
    parts/parts
    modifier/modifier
    api/modules
+   changelog/changelog
 
 
 .. only:: html

docs/requirements.txt

@@ -4,3 +4,4 @@ shapely
 scipy
 qrcode
 descartes
+m2r2

gdshelpers/__init__.py

@@ -11,4 +11,4 @@
 
 configuration = _Configuration()
 
-__version__ = '1.1.3'
+__version__ = '1.2.0'

gdshelpers/export/gdsii_export.py

@@ -9,7 +9,7 @@
 from io import BytesIO
 import numpy as np
 
-from shapely.geometry import Polygon
+from shapely.geometry import Polygon, LineString
 
 
 def _real_to_8byte(value):
@@ -28,25 +28,31 @@ def _cell_to_gdsii_binary(cell, grid_steps_per_unit, max_points, max_line_points
         b.write(pack('>2H', 4 + len(name), 0x0606) + name.encode('ascii'))  # STRNAME STRING cell_name
 
         for layer, polygons in cell.get_fractured_layer_dict(max_points, max_line_points).items():
-            for polygon in polygons:
-                if not isinstance(polygon, Polygon):
+            for shapely_object in polygons:
+                if isinstance(shapely_object, Polygon):
+                    if shapely_object.interiors:
+                        raise AssertionError('GDSII only supports polygons without holes')
+                    coords = list(shapely_object.exterior.coords) + [shapely_object.exterior.coords[0]]
+                    b.write(pack('>8H', 4, 0x0800,  # BOUNDARY NO_DATA
+                                 6, 0x0D02, layer,  # LAYER INTEGER_2 layer
+                                 6, 0x0E02, layer))  # DATATYPE INTEGER_2 datatype
+                elif isinstance(shapely_object, LineString):
+                    coords = shapely_object.coords
+                    b.write(pack('>8H', 4, 0x0900,  # PATH NO_DATA
+                                 6, 0x0D02, layer,  # LAYER INTEGER_2 layer
+                                 6, 0x0E02, layer))  # DATATYPE INTEGER_2 datatype
+                else:
                     import warnings
                     warnings.warn(
-                        'Shapely object of type ' + str(type(polygon)) + ' not convertible to GDSII, skipping...')
+                        'Shapely object of type ' + str(
+                            type(shapely_object)) + ' not convertible to GDSII, skipping...')
                     continue
-                if polygon.interiors:
-                    raise AssertionError('GDSII only supports polygons without holes')
-                xy = np.round(
-                    np.array(
-                        list(polygon.exterior.coords) + [polygon.exterior.coords[0]]) * grid_steps_per_unit).astype(
-                    '>i4')
-                b.write(pack('>8H', 4, 0x0800,  # BOUNDARY NO_DATA
-                             6, 0x0D02, layer,  # LAYER INTEGER_2 layer
-                             6, 0x0E02, layer))  # DATATYPE INTEGER_2 datatype
+
+                xy = np.round(np.array(coords) * grid_steps_per_unit).astype('>i4')
                 for start in range(0, xy.shape[0], 8191):  # Split in Blocks of 8191 points
                     stop = min(start + 8191, xy.shape[0])
                     b.write(pack('>2H', 4 + 8 * (stop - start), 0x1003))  # XY INTEGER_4
-                    b.write(xy[start:stop].tobytes())  # coords of polygon
+                    b.write(xy[start:stop].tobytes())  # coords of shapely_object
                 b.write(pack('>2H', 4, 0x1100))  # ENDEL NO_DATA
 
         for ref in cell.cells:
@@ -62,7 +68,7 @@ def _cell_to_gdsii_binary(cell, grid_steps_per_unit, max_points, max_line_points
                 if ref['magnification'] is not None:
                     b.write(pack('>2H', 12, 0x1B05) + _real_to_8byte(ref['magnification']))  # MAG REAL_8
                 if ref['angle'] is not None:
-                    b.write(pack('>2H', 12, 0x1C05) + _real_to_8byte(np.rad2deg(ref['angle'])))  # ANGLE REAL_8
+                    b.write(pack('>2H', 12, 0x1C05) + _real_to_8byte(np.rad2deg(ref['angle']) % 360.))  # ANGLE REAL_8
             if aref:
                 b.write(pack('>2H2h', 8, 0x1302, ref['columns'], ref['rows']))  # COLROW INTEGER_2 spacing
             b.write(pack('>2H', 28 if aref else 12, 0x1003) + np.round(
@@ -84,7 +90,7 @@ def _cell_to_gdsii_binary(cell, grid_steps_per_unit, max_points, max_line_points
 
 
 def write_cell_to_gdsii_file(outfile, cell, unit=1e-6, grid_steps_per_unit=1000, max_points=4000, max_line_points=4000,
-                             timestamp=None, parallel=False):
+                             timestamp=None, parallel=False, max_workers=None):
     name = 'gdshelpers_exported_library'
     grid_step_unit = unit / grid_steps_per_unit
     timestamp = datetime.datetime.now() if timestamp is None else timestamp
@@ -113,7 +119,7 @@ def add_cells_to_unique_list(start_cell):
     # UNITS REAL_8 1/grid_steps_per_unit grid_step_unit
     if parallel:
         from concurrent.futures import ProcessPoolExecutor
-        with ProcessPoolExecutor() as pool:
+        with ProcessPoolExecutor(max_workers=max_workers) as pool:
             num = len(cells)
             for binary in pool.map(_cell_to_gdsii_binary, cells, (grid_steps_per_unit,) * num, (max_points,) * num,
                                    (max_line_points,) * num, (timestamp,) * num):
@@ -141,6 +147,8 @@ def add_cells_to_unique_list(start_cell):
     sub_cell = Cell('sub_cell')
     sub_cell.add_to_layer(1, waveguide)
 
+    sub_cell.add_to_layer(3, LineString(((0, 0), (100, 100))))
+
     device_cell.add_cell(sub_cell, origin=(10, 10), angle=np.pi / 2)
 
     with open('gdsii_export.gds', 'wb') as file:

gdshelpers/geometry/chip.py

@@ -115,11 +115,13 @@ def add_cell(self, cell, origin=(0, 0), angle: Optional[float] = None, columns=1
         :param rows: Number of rows
         :param spacing: Spacing between the cells, should be an array in the form [x_spacing, y_spacing]
         """
-        if cell.name in [cell_dict['cell'].name for cell_dict in self.cells]:
-            import warnings
-            warnings.warn(
+        if cell.get_dlw_data() and cell.name in [cell_dict['cell'].name for cell_dict in self.cells]:
+            raise ValueError(
                 'Cell name "{cell_name:s}" added multiple times to {self_name:s}.'
-                ' Can be problematic for desc/dlw-files'.format(cell_name=cell.name, self_name=self.name))
+                ' This is not allowed for cells containing DLW data.'.format(
+                    cell_name=cell.name, self_name=self.name
+                )
+            )
         self.cells.append(
             dict(cell=cell, origin=origin, angle=angle, magnification=None, x_reflection=False, columns=columns,
                  rows=rows, spacing=spacing))
@@ -190,10 +192,13 @@ def get_dlw_data(self):
         dlw_data = self.dlw_data.copy()
         for sub_cell in self.cells:
             cell, origin = sub_cell['cell'], sub_cell['origin']
-
             for dlw_type, dlw_type_data in cell.get_dlw_data().items():
                 for dlw_id, data in dlw_type_data.items():
                     data = data.copy()
+                    if sub_cell['angle'] is not None:
+                        c, s = np.cos(sub_cell['angle']), np.sin(sub_cell['angle'])
+                        data['origin'] = np.array([[c, -s], [s, c]]).dot(data['origin'])
+                        data['angle'] += sub_cell['angle']
                     data['origin'] = (np.array(origin) + data['origin']).tolist()
                     if dlw_type not in dlw_data:
                         dlw_data[dlw_type] = {}
@@ -292,7 +297,7 @@ def start_viewer(self):
         import gdspy
         gdspy.LayoutViewer(library=self.get_gdspy_lib(), depth=10)
 
-    def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=False):
+    def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=False, max_workers=None):
         """
         Exports the layout and creates an DLW-file, if DLW-features are used.
 
@@ -305,6 +310,8 @@ def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=Fal
         :param parallel: Defines if parallelization is used (only supported in Python 3).
             Standard value will be changed to True in a future version.
             Deactivating can be useful for debugging reasons.
+        :param max_workers: If parallel is True, this can be used to limit the number of parallel processes.
+            This can be useful if you run into out-of-memory errors otherwise.
         """
 
         if library is not None:
@@ -317,8 +324,8 @@ def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=Fal
         elif name.endswith('.gds'):
             name = name[:-4]
             library = library or 'gdshelpers'
-        elif name.endswith('.oasis'):
-            name = name[:-6]
+        elif name.endswith('.oas'):
+            name = name[:-4]
             library = library or 'fatamorgana'
         elif name.endswith('.dxf'):
             name = name[:-4]
@@ -331,15 +338,16 @@ def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=Fal
             import shutil
 
             with NamedTemporaryFile('wb', delete=False) as tmp:
-                write_cell_to_gdsii_file(tmp, self, grid_steps_per_unit=grid_steps_per_micron, parallel=parallel)
+                write_cell_to_gdsii_file(tmp, self, grid_steps_per_unit=grid_steps_per_micron, parallel=parallel,
+                                         max_workers=max_workers)
             shutil.move(tmp.name, name + '.gds')
 
         elif library == 'gdspy':
             import gdspy
 
             if parallel:
                 from concurrent.futures import ProcessPoolExecutor
-                with ProcessPoolExecutor() as pool:
+                with ProcessPoolExecutor(max_workers=max_workers) as pool:
                     self.get_gdspy_cell(pool)
             else:
                 self.get_gdspy_cell()
@@ -348,7 +356,7 @@ def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=Fal
             gdspy_cells = self.get_gdspy_lib().cell_dict.values()
             if parallel:
                 from concurrent.futures import ProcessPoolExecutor
-                with ProcessPoolExecutor() as pool:
+                with ProcessPoolExecutor(max_workers=max_workers) as pool:
                     binary_cells = pool.map(gdspy.Cell.to_gds, gdspy_cells, [grid_steps_per_micron] * len(gdspy_cells))
             else:
                 binary_cells = map(gdspy.Cell.to_gds, gdspy_cells, [grid_steps_per_micron] * len(gdspy_cells))
@@ -360,31 +368,13 @@ def save(self, name=None, library=None, grid_steps_per_micron=1000, parallel=Fal
 
             if parallel:
                 from concurrent.futures import ProcessPoolExecutor
-                with ProcessPoolExecutor() as pool:
+                with ProcessPoolExecutor(max_workers=max_workers) as pool:
                     cells = self.get_oasis_cells(grid_steps_per_micron, pool)
             else:
                 cells = self.get_oasis_cells(grid_steps_per_micron)
 
             layout.cells = [cells[0]] + list(set(cells[1:]))
 
-            # noinspection PyUnresolvedReferences
-            def replace_names_by_ids(oasis_layout):
-                name_id = {}
-                for cell_id, cell in enumerate(oasis_layout.cells):
-                    if cell.name.string in name_id:
-                        raise RuntimeError(
-                            'Each cell name should be unique, name "' + cell.name.string + '" is used multiple times')
-                    name_id[cell.name.string] = cell_id
-                    cell.name = cell_id
-                for cell in oasis_layout.cells:
-                    for placement in cell.placements:
-                        placement.name = name_id[placement.name.string]
-
-                oasis_layout.cellnames = {v: k for k, v in name_id.items()}
-
-            # improves performance for reading oasis file and workaround for fatamorgana-bug
-            replace_names_by_ids(layout)
-
             with open(name + '.oas', 'wb') as f:
                 layout.write(f)
         elif library == 'ezdxf':
@@ -407,7 +397,7 @@ def save_desc(self, filename: str):
         """
         if not filename.endswith('.desc'):
             filename += '.desc'
-        with open(filename + '.desc', 'w') as f:
+        with open(filename, 'w') as f:
             json.dump(self.get_desc(), f, indent=True)
 
     def get_reduced_layer(self, layer: int):
@@ -547,7 +537,7 @@ def add_dlw_marker(self, label: str, layer: int, origin):
         self.add_to_layer(layer, DLWMarker(origin))
         self.add_to_layer(std_layers.parnamelayer1, Text(origin, 2, label, alignment='center-center'))
 
-        self.add_dlw_data('marker', label, {'origin': list(origin)})
+        self.add_dlw_data('marker', label, {'origin': list(origin), 'angle': 0})
 
     def add_dlw_taper_at_port(self, label: str, layer: int, port: Port, taper_length: float, tip_width=.01,
                               with_markers=True):

gdshelpers/parts/waveguide.py

@@ -280,7 +280,7 @@ def find_y(y):
             poly_path = np.concatenate([poly_path_1, poly_path_2[::-1, :]])
 
             assert shapely.geometry.LineString(poly_path).is_simple, \
-                'Outer lines of parameterized wg intersect. Try using lower bend radii or smaller a smaller wg'
+                'Outer lines of parameterized wg intersect. Try using larger bend radii or smaller a smaller wg'
 
             # Now add the shapely objects and do book keeping
             polygon = shapely.geometry.Polygon(poly_path)