setupEM 0.10.2__tar.gz → 0.11.1__tar.gz

setupem-0.11.1/PKG-INFO

@@ -0,0 +1,26 @@
+Metadata-Version: 2.4
+Name: setupEM
+Version: 0.11.1
+Summary: Python tool for configuration of gds2palace workflow with GUI.
+Author-email: Volker Muehlhaus <volker@muehlhaus.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/VolkerMuehlhaus/setupEM
+Project-URL: Repository, https://github.com/VolkerMuehlhaus/setupEM
+Project-URL: Changelog, https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: gds2palace>=0.8.0
+Requires-Dist: gds_prepare_for_EM>=1.3.0
+Requires-Dist: PySide6
+Requires-Dist: shiboken6
+Requires-Dist: scipy
+Requires-Dist: requests
+Requires-Dist: scikit-rf
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: gdspy
+Requires-Dist: meshio
+Requires-Dist: pyvista
+Requires-Dist: pyvistaqt
+Dynamic: license-file

{setupem-0.10.2 → setupem-0.11.1}/README.md

@@ -251,7 +251,7 @@ Once field-dump results are available (Palace: set `fdump`; Elmer: enable field
 
 The built-in viewer has a single, axis-aligned clip plane (X/Y/Z + a position slider, shown in µm) to see a cross-section through the model, rather than a free-orientation drag-widget - **Find max.** jumps the plane straight to the largest value of the currently selected field along that axis. Standard CAD/ParaView-style **+X/-X/+Y/-Y/+Z/-Z** buttons snap the camera to look straight down each axis; the clip plane's kept side follows whichever of these you last used for its axis, so the exposed cut face always faces the camera instead of occasionally showing the model's untouched exterior surface.
 
-The **Field** panel picks which array to color by, defaulting to E-field magnitude (log color scale) for Palace and Elmer-as-EM-solver mode, or temperature (linear) for Elmer thermal - the Min/Max fields let you override the color range manually, with a button to reset back to the data's own range. **Display** controls opacity (to see a hotspot through the surrounding material without losing the outer shape as context) and a mesh-edge overlay. If more than one equally-valid result file exists (e.g. Palace's main "driven" field dump and its separate "driven_boundary" one), a **Result File** picker lets you choose between them instead of guessing.
+The **Field** panel picks which array to color by, defaulting to E-field magnitude (log color scale) for Palace and Elmer-as-EM-solver mode, or temperature (linear) for Elmer thermal - the Min/Max fields let you override the color range manually, with a button to reset back to the data's own range. With the log color scale, a Range dropdown (-10 to -70 dB below Max, default -70 dB) replaces the Min field. **Display** controls opacity (to see a hotspot through the surrounding material without losing the outer shape as context) and a mesh-edge overlay. If more than one equally-valid result file exists (e.g. Palace's main "driven" field dump and its separate "driven_boundary" one), a **Result File** picker lets you choose between them instead of guessing.
 
 For a vector array (E/B-field, Poynting vector `S`, ...), **Show arrows** overlays direction arrows on top of the color, auto-scaled from the field's own magnitude on a log scale so both weak and strong regions stay visible instead of only the single hottest point - the **Arrow size** slider (0.5% steps) scales them to taste, and also controls how densely they're packed in, since smaller arrows can sit closer together than large ones without turning into a solid block.
 

{setupem-0.10.2 → setupem-0.11.1}/pyproject.toml

@@ -13,7 +13,7 @@ authors = [
 ]
 dependencies = [
     "gds2palace>=0.8.0",
-    "gds_prepare_for_EM>=1.2.0",
+    "gds_prepare_for_EM>=1.3.0",
     "PySide6",
     "shiboken6",
     "scipy",

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/__init__.py

@@ -24,4 +24,4 @@ A Python tool for EM setup using gds2palace.
 from .setupEM import main
 
 __all__ = ["main"]
-__version__ = "0.10.2"
+__version__ = "0.11.1"

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/field_viewer.py

@@ -63,7 +63,7 @@ from pyvistaqt import QtInteractor
 from PySide6.QtWidgets import (
     QApplication, QDialog, QVBoxLayout, QHBoxLayout, QGridLayout, QGroupBox,
     QLabel, QPushButton, QRadioButton, QButtonGroup, QCheckBox,
-    QSlider, QComboBox, QLineEdit, QStyleFactory, QColorDialog, QMenu,
+    QSlider, QComboBox, QLineEdit, QStyleFactory, QColorDialog, QMenu, QWidget,
 )
 from PySide6.QtCore import Qt, QThread, QTimer, Signal
 from PySide6.QtGui import QShortcut, QKeySequence, QColor
@@ -527,6 +527,25 @@ def _is_field_amplitude_array(array_name):
     return array_name in _FIELD_AMPLITUDE_ARRAYS
 
 
+# Log color scale range below the maximum, offered in the "Range" dropdown -
+# see FieldViewerWindow._get_clim(). The last entry is the default.
+_LOG_RANGE_DB_CHOICES = (10, 20, 30, 40, 50, 60, 70)
+_LOG_RANGE_DB_DEFAULT = 70
+
+# Two meshes with bounding boxes this close (fraction of the diagonal) count
+# as the same geometry when switching result files: camera and clip position
+# are kept - see FieldViewerWindow._switch_to_file().
+_SAME_BOUNDS_TOLERANCE = 1e-3
+
+
+def _db_floor(array_name, clim_max, db_range):
+    """Lower color limit db_range dB below clim_max: 20*log10 convention for
+    E/B-field arrays, 10*log10 for everything else - see
+    _is_field_amplitude_array()."""
+    db_per_decade = 20.0 if _is_field_amplitude_array(array_name) else 10.0
+    return clim_max / 10.0 ** (db_range / db_per_decade)
+
+
 def _db_range_to_clim(mesh, array_name, db_range):
     """(floor, data_max) for a log color scale spanning db_range dB below
     array_name's own maximum in mesh, using the field-amplitude convention
@@ -539,9 +558,7 @@ def _db_range_to_clim(mesh, array_name, db_range):
     if positive.size == 0:
         return None
     data_max = positive.max()
-    db_per_decade = 20.0 if _is_field_amplitude_array(array_name) else 10.0
-    floor = data_max / 10.0 ** (db_range / db_per_decade)
-    return floor, data_max
+    return _db_floor(array_name, data_max, db_range), data_max
 
 
 # ------------------------------------------------------------------
@@ -623,6 +640,13 @@ class FieldViewerWindow(QDialog):
         # leaves the scene briefly actor-less, and PyVista's own "reset camera if
         # this looks like the first mesh" heuristic was firing on every redraw.
         self._camera_needs_reset = True
+        # Field type the user picked in the Field combo (and its log scale /
+        # colormap), restored on a cycle or file switch whenever the new data
+        # has an array of that name - even after a cycle or file in between
+        # lacked it and fell back to a default. See _load_mesh().
+        self._preferred_array = None
+        self._preferred_log = None
+        self._preferred_cmap = None
 
         # Colors for mesh edges / vector arrows / scalar-bar (legend) text,
         # each changeable via a small swatch button next to its checkbox in
@@ -689,6 +713,7 @@ class FieldViewerWindow(QDialog):
         self._redraw_scheduled = False
 
         self._build_ui()
+        self._update_range_controls()
         self._load_mesh()
         # Same generic starting view for every source: full mesh, no clip - the
         # "Find max." button (see _move_slider_to_max()) is one click away for
@@ -902,9 +927,12 @@ class FieldViewerWindow(QDialog):
         field_layout = QVBoxLayout()
         self.array_combo = QComboBox()
         self.array_combo.currentTextChanged.connect(self._on_array_changed)
+        # user selection only (not programmatic changes): remembered as the preferred field type
+        self.array_combo.textActivated.connect(self._remember_field_choice)
         field_layout.addWidget(self.array_combo)
         self.log_scale_cb = QCheckBox("Log color scale")
-        self.log_scale_cb.toggled.connect(self._on_redraw_needed)
+        self.log_scale_cb.toggled.connect(self._on_log_scale_toggled)
+        self.log_scale_cb.clicked.connect(self._remember_field_choice)
         field_layout.addWidget(self.log_scale_cb)
 
         # Color range (Min/Max/Reset) directly below the array/log-scale
@@ -913,12 +941,32 @@ class FieldViewerWindow(QDialog):
         # Min/Max stacked one per row (not side by side) - two QLineEdits
         # sharing one row left each too narrow to read its own value
         # comfortably, given the whole Field group's fixed column width.
-        min_layout = QHBoxLayout()
+        # Linear scale: Min field. Log scale: "Range" dropdown instead, the
+        # lower limit is that many dB below Max - see _get_clim(). Only one
+        # of the two rows is visible, see _update_range_controls().
+        self.clim_min_row = QWidget()
+        min_layout = QHBoxLayout(self.clim_min_row)
+        min_layout.setContentsMargins(0, 0, 0, 0)
         min_layout.addWidget(QLabel("Min:"))
         self.clim_min_edit = QLineEdit()
         self.clim_min_edit.editingFinished.connect(self._on_redraw_needed)
         min_layout.addWidget(self.clim_min_edit)
-        field_layout.addLayout(min_layout)
+        field_layout.addWidget(self.clim_min_row)
+
+        self.log_range_row = QWidget()
+        log_range_layout = QHBoxLayout(self.log_range_row)
+        log_range_layout.setContentsMargins(0, 0, 0, 0)
+        log_range_layout.addWidget(QLabel("Range:"))
+        self.log_range_combo = QComboBox()
+        for db in _LOG_RANGE_DB_CHOICES:
+            self.log_range_combo.addItem(f"-{db} dB", db)
+        self.log_range_combo.setCurrentIndex(_LOG_RANGE_DB_CHOICES.index(_LOG_RANGE_DB_DEFAULT))
+        self.log_range_combo.setToolTip(
+            "Log color scale: show values down to this many dB below Max "
+            "(20*log10 for E/B fields, 10*log10 for power-like arrays such as S)")
+        self.log_range_combo.currentIndexChanged.connect(self._on_redraw_needed)
+        log_range_layout.addWidget(self.log_range_combo)
+        field_layout.addWidget(self.log_range_row)
 
         max_layout = QHBoxLayout()
         max_layout.addWidget(QLabel("Max:"))
@@ -1124,22 +1172,34 @@ class FieldViewerWindow(QDialog):
         hidden again)."""
         if path == self.file_path:
             return
+        old_bounds = np.array(self._full_mesh.bounds) if self._full_mesh is not None else None
         self.file_path = path
         self._load_error = None
         self.warning_label.setText("")
-        # A different result file can have entirely different geometry/bounds
-        # (e.g. Palace's "driven" vs. "driven_boundary") - unlike every other
-        # control in this window, this is a good reason to re-fit the camera
-        # rather than keep the previous file's pan/zoom/rotation.
-        self._camera_needs_reset = True
         # Default to the NEW file's own first cycle - a cycle index picked on
         # the old file has no guaranteed correspondence here (different files
         # can have different cycle counts), see __init__'s self._cycle_index.
         self._cycle_index = None
         self._cycles_without_data = set()
         self._cycle_labels = None
-        self._load_mesh()
-        self._on_axis_changed()  # resets the clip slider for the new mesh's bounds, redraws
+        # keep the field type if the new file has the same array, see _load_mesh()
+        self._load_mesh(preserve_selection=True, keep_range=False)
+        # Same geometry (e.g. another AMR iteration or frequency file of the
+        # same model): keep the camera (view direction, pan, zoom) and the clip
+        # position. Different bounds (e.g. Palace's "driven" vs.
+        # "driven_boundary" of a different domain): re-fit the camera and
+        # re-center the clip slider for the new mesh.
+        new_bounds = np.array(self._full_mesh.bounds) if self._full_mesh is not None else None
+        same_geometry = (
+            old_bounds is not None and new_bounds is not None
+            and np.allclose(old_bounds, new_bounds,
+                            atol=_SAME_BOUNDS_TOLERANCE * max(self._full_mesh.length, 1e-30))
+        )
+        if same_geometry:
+            self._schedule_redraw()
+        else:
+            self._camera_needs_reset = True
+            self._on_axis_changed()  # resets the clip slider for the new mesh's bounds, redraws
 
     def _on_cycle_changed(self, index):
         """Switch which solved cycle (e.g. frequency, for a multi-frequency
@@ -1151,7 +1211,7 @@ class FieldViewerWindow(QDialog):
         if index < 0 or index == self._cycle_index:
             return
         self._cycle_index = index
-        self._load_mesh(preserve_selection=True)
+        self._load_mesh(preserve_selection=True, keep_range=True)
         self._schedule_redraw()
 
     def _on_include_iterations_toggled(self, checked):
@@ -1169,15 +1229,18 @@ class FieldViewerWindow(QDialog):
 
     # ---------- Mesh loading ----------
 
-    def _load_mesh(self, preserve_selection=False):
+    def _load_mesh(self, preserve_selection=False, keep_range=True):
         """Load self._full_mesh from self.file_path/self._cycle_index.
 
-        preserve_selection=True (only passed by _on_cycle_changed()) keeps
-        the current array/color-by selection instead of recomputing a
-        default - array names are the same across cycles of one file, only
-        the underlying values/ranges differ per cycle. Every other caller
-        (initial load, _switch_to_file()) leaves this False, unchanged from
-        before this parameter existed.
+        preserve_selection=True (passed by _on_cycle_changed() and
+        _switch_to_file()) keeps the current array/color-by selection and log
+        scale setting if the newly loaded data has an array of the same name,
+        instead of recomputing a default. The initial load leaves this False.
+
+        keep_range=True (cycle switch) keeps a linear scale's manually entered
+        Min/Max; keep_range=False (file switch) resets them to the new data.
+        A log scale's Max is always reset to the new data's maximum, since its
+        dB range is defined relative to the maximum.
         """
         self.setWindowTitle(f"Field Viewer - {self._file_labels[self.file_path]}")
         # Bump the generation before anything else below - see __init__'s
@@ -1245,16 +1308,35 @@ class FieldViewerWindow(QDialog):
         self.array_combo.addItems(available)
         self.array_combo.blockSignals(False)
 
-        if preserve_selection and previous_array in available:
-            # Keep the user's current settings across a cycle-only switch -
-            # not just which array is selected, but also its Min/Max color
-            # range: don't let _on_array_changed's _reset_clim_range() (fired
+        # The user's own field choice first, then whatever is shown now (e.g. a
+        # default the user kept), then the default for this data.
+        if preserve_selection and self._preferred_array in available:
+            target_array = self._preferred_array
+        elif preserve_selection and previous_array in available:
+            target_array = previous_array
+        else:
+            target_array = None
+        if target_array is not None:
+            # Keep the user's current settings across a switch - not just which
+            # array is selected, but also its Min/Max color range on a cycle
+            # switch: don't let _on_array_changed's _reset_clim_range() (fired
             # by setCurrentText() below re-selecting the same array name in
             # the freshly repopulated combo) clobber a manually-entered range
             # with this cycle's own data range.
             self.array_combo.blockSignals(True)
-            self.array_combo.setCurrentText(previous_array)
+            self.array_combo.setCurrentText(target_array)
             self.array_combo.blockSignals(False)
+            if target_array == self._preferred_array and target_array != previous_array:
+                # back to the user's choice after a fallback: its own scale settings
+                self._current_cmap = self._preferred_cmap
+                self.log_scale_cb.blockSignals(True)
+                self.log_scale_cb.setChecked(self._preferred_log)
+                self.log_scale_cb.blockSignals(False)
+                self._update_range_controls()
+            if not keep_range or target_array != previous_array:
+                self._reset_clim_range()
+            elif self.log_scale_cb.isChecked():
+                self._reset_clim_max()
             self._update_vector_checkbox_state()
             return
 
@@ -1263,6 +1345,7 @@ class FieldViewerWindow(QDialog):
         self.log_scale_cb.blockSignals(True)
         self.log_scale_cb.setChecked(default_log_scale)
         self.log_scale_cb.blockSignals(False)
+        self._update_range_controls()
         if default_array is not None:
             self.array_combo.setCurrentText(default_array)
             # Explicit calls, not just relying on currentTextChanged above: that
@@ -1464,6 +1547,13 @@ class FieldViewerWindow(QDialog):
 
     # ---------- Field/array picker ----------
 
+    def _remember_field_choice(self, _value=None):
+        """Remember the field type (array, log scale, colormap) the user picked,
+        see __init__'s self._preferred_array."""
+        self._preferred_array = self.array_combo.currentText() or None
+        self._preferred_log = self.log_scale_cb.isChecked()
+        self._preferred_cmap = self._current_cmap
+
     def _on_array_changed(self, _text=None):
         self._reset_clim_range()
         self._update_vector_checkbox_state()
@@ -1514,19 +1604,56 @@ class FieldViewerWindow(QDialog):
         self.clim_min_edit.setText(f"{magnitudes.min():.6g}")
         self.clim_max_edit.setText(f"{magnitudes.max():.6g}")
 
+    def _reset_clim_max(self):
+        """Set only Max to the selected array's data maximum - a log scale's
+        lower limit follows from Max and the dB range, see _get_clim()."""
+        array_name = self.array_combo.currentText()
+        if self._full_mesh is None or not array_name or array_name not in self._full_mesh.point_data:
+            return
+        magnitudes = _array_magnitudes(self._full_mesh[array_name])
+        if magnitudes.size:
+            self.clim_max_edit.setText(f"{magnitudes.max():.6g}")
+
     def _on_clim_reset_clicked(self):
         self._reset_clim_range()
         self._schedule_redraw()
 
+    def _update_range_controls(self):
+        """Log scale: show the dB "Range" dropdown instead of the Min field."""
+        log = self.log_scale_cb.isChecked()
+        self.clim_min_row.setVisible(not log)
+        self.log_range_row.setVisible(log)
+
+    def _on_log_scale_toggled(self, _checked=None):
+        self._update_range_controls()
+        self._schedule_redraw()
+
+    def _set_log_range_db(self, db_range):
+        """Select db_range in the dB dropdown, adding it if it isn't one of the
+        standard choices (e.g. from the CLI's --log-range-db)."""
+        index = self.log_range_combo.findData(db_range)
+        if index < 0:
+            self.log_range_combo.addItem(f"-{db_range:g} dB", db_range)
+            index = self.log_range_combo.count() - 1
+        self.log_range_combo.setCurrentIndex(index)
+
     def _get_clim(self):
         """(min, max) parsed from the Min/Max fields, or None to let PyVista
         auto-scale from the currently displayed mesh (matches the behavior before
         this control existed). Invalid/empty text, or min >= max, both fall back
         to None rather than raising or blocking the redraw - VTK's own clim
-        requires min < max, and a typo here shouldn't break the view."""
+        requires min < max, and a typo here shouldn't break the view.
+
+        Log scale: min is the dB "Range" below Max instead of the Min field."""
         try:
-            clim_min = float(self.clim_min_edit.text())
             clim_max = float(self.clim_max_edit.text())
+            if self.log_scale_cb.isChecked():
+                if clim_max <= 0:
+                    return None
+                clim_min = _db_floor(self.array_combo.currentText(), clim_max,
+                                     self.log_range_combo.currentData())
+            else:
+                clim_min = float(self.clim_min_edit.text())
         except ValueError:
             return None
         if clim_min >= clim_max:
@@ -1901,7 +2028,9 @@ def main():
                               "thermal only). Ignored if --array is also given.")
     parser.add_argument("--array", help="exact point-data array name to color by "
                                          "(e.g. E_imag, U_e, B_imag) - overrides --field")
-    parser.add_argument("--log-scale", action="store_true", help="use a log color scale")
+    parser.add_argument("--log-scale", action="store_true",
+                         help=f"use a log color scale, down to {_LOG_RANGE_DB_DEFAULT} dB below the "
+                              "maximum unless --log-range-db is given")
     parser.add_argument("--log-range-db", type=float,
                          help="set the color range's minimum this many dB below the "
                               "data's own maximum (implies --log-scale) instead of using "
@@ -2008,12 +2137,10 @@ def main():
         window.log_scale_cb.setChecked(True)
     if args.log_range_db is not None:
         array_name = window.array_combo.currentText()
-        result = _db_range_to_clim(window._full_mesh, array_name, args.log_range_db)
-        if result is None:
+        if _db_range_to_clim(window._full_mesh, array_name, args.log_range_db) is None:
             die(f"--log-range-db: array {array_name!r} has no positive values to scale from")
-        floor, data_max = result
-        window.clim_min_edit.setText(f"{floor:.6g}")
-        window.clim_max_edit.setText(f"{data_max:.6g}")
+        window._set_log_range_db(args.log_range_db)
+        window._reset_clim_max()
         window._redraw()
 
     if args.opacity is not None:

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/setupEM.py

@@ -3210,7 +3210,7 @@ class PreferencesDialog(QDialog):
         self.simplify_excluded_layers_edit = add_row(
             simplify_form, "Layers excluded from simplification", "simplify_excluded_layers", "")
         self.simplify_excluded_layers_edit.setPlaceholderText("e.g. 10,11 - blank = none")
-        self.simplify_merge_per_layer_checkbox = QCheckBox("Merge polygons per layer (final step)")
+        self.simplify_merge_per_layer_checkbox = QCheckBox("Merge polygons per layer")
         self.simplify_merge_per_layer_checkbox.setChecked(
             get_preference_bool(self.app_name, "simplify_merge_per_layer", True))
         simplify_form.addWidget(self.simplify_merge_per_layer_checkbox)

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/setupThermal.py

@@ -1225,7 +1225,7 @@ class PreferencesDialog(QDialog):
         self.simplify_excluded_layers_edit = add_row(
             simplify_form, "Layers excluded from simplification", "simplify_excluded_layers", "")
         self.simplify_excluded_layers_edit.setPlaceholderText("e.g. 10,11 - blank = none")
-        self.simplify_merge_per_layer_checkbox = QCheckBox("Merge polygons per layer (final step)")
+        self.simplify_merge_per_layer_checkbox = QCheckBox("Merge polygons per layer")
         self.simplify_merge_per_layer_checkbox.setChecked(
             get_preference_bool(self.app_name, "simplify_merge_per_layer", True))
         simplify_form.addWidget(self.simplify_merge_per_layer_checkbox)

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/setup_common.py

@@ -474,6 +474,40 @@ def resolve_value_text(value_text, known_constants):
     return eval_simple_python_expression(node, known_constants)
 
 
+def normalize_purpose_list(value, default=(0,)):
+    # Normalize a GDSII purpose (datatype) value to the flat list of ints that
+    # gds_reader.read_gds() expects as purposelist ("purpose in purposelist").
+    # Accepts an int, comma-separated text ("0, 35, 4", also "[0]" or "(0, 35)"),
+    # or a list/tuple. Nested lists/tuples are flattened, so values stored by
+    # older versions as [(0, 35, 4)] (or [[0, 35, 4]] after a JSON round trip)
+    # load back correctly instead of matching no datatype at all. Empty or
+    # unparseable input returns the default.
+    if isinstance(value, str):
+        text = value.strip()
+        if not text:
+            return list(default)
+        try:
+            value = ast.literal_eval('[' + text + ']')
+        except (SyntaxError, ValueError):
+            return list(default)
+
+    result = []
+    pending = [value]
+    while pending:
+        item = pending.pop(0)
+        if isinstance(item, (list, tuple)):
+            pending[0:0] = list(item)
+        elif isinstance(item, bool):
+            return list(default)
+        elif isinstance(item, int):
+            result.append(item)
+        elif isinstance(item, float) and item.is_integer():
+            result.append(int(item))
+        else:
+            return list(default)
+    return result if result else list(default)
+
+
 def parse_assignments(file_path):
     # parse lines from a Python model code for variable assigments
     parameters = {}
@@ -1090,10 +1124,9 @@ class FileInputTab(QWidget):
         self.preprocess_gds_checkbox.setChecked(bool(get_saved_value(saved_values, "preprocess_gds", True)))
 
         purpose_default = get_preference(self.MainWindow.APP_NAME, "purpose", "0")
-        int_list = saved_values.get("purpose", purpose_default)
-        purpose_string = str(int_list).replace('[', '').replace(']', '')
-        self.purpose_edit.setText(purpose_string)
-        # self.purpose_edit.setText(','.join(map(str, int_list)))
+        int_list = normalize_purpose_list(saved_values.get("purpose", purpose_default),
+                                          default=normalize_purpose_list(purpose_default))
+        self.purpose_edit.setText(', '.join(map(str, int_list)))
 
         # read_XML(self.XML_file_edit.text()) # safe if invalid filename
 
@@ -1121,13 +1154,10 @@ class FileInputTab(QWidget):
             # a gds2palace that doesn't support this setting for this application
             saved_values.pop("fill_factor_correction", None)
 
-        text = self.purpose_edit.text()
-        if text != "":
-            # save as list of comma separated values
-            saved_values["purpose"] = ast.literal_eval('[' + text + ']')
-        else:
-            purpose_default = get_preference(self.MainWindow.APP_NAME, "purpose", "0")
-            saved_values["purpose"] = ast.literal_eval('[' + str(purpose_default) + ']')
+        # save as flat list of ints, empty text falls back to the preference default
+        purpose_default = get_preference(self.MainWindow.APP_NAME, "purpose", "0")
+        saved_values["purpose"] = normalize_purpose_list(self.purpose_edit.text(),
+                                                         default=normalize_purpose_list(purpose_default))
 
         # also trigger the load function of CreateModelTab, because that uses gds file info
         self.MainWindow.create_model_tab.load_values()
@@ -4210,7 +4240,7 @@ class MainWindowBase(QMainWindow):
                 saved_values.clear()
                 # set values that are not included in import
                 saved_values["unit"] = 1e-6
-                saved_values["purpose"] = 0
+                saved_values["purpose"] = [0]
 
                 # check what directory the Python code is in, we might use that to prefix gdsfile and XML file
                 modelcode_path = os.path.dirname(file_path)
@@ -4236,6 +4266,15 @@ class MainWindowBase(QMainWindow):
                                     if not isinstance(values, (list, tuple)):
                                         values = [values]
                                     saved_values[varname] = [f / 1e9 for f in values]
+                                elif varname == "purpose":
+                                    # scalar or list in the script, always a flat list here
+                                    # (stripping "[]" and resolving would give a tuple for
+                                    # [0, 35, 4], which then never matched any datatype)
+                                    try:
+                                        value = resolve_value_text(import_value, known_constants)
+                                    except (SyntaxError, ValueError, TypeError, ZeroDivisionError):
+                                        value = import_value
+                                    saved_values[varname] = normalize_purpose_list(value)
                                 elif varname in ("variable_overrides", "refined_cellsize_override"):
                                     saved_values[varname] = resolve_value_text(import_value, known_constants)
                                 elif varname in ["gds_filename", "XML_filename", "GdsFile", "SubstrateFile"]:
@@ -4543,11 +4582,7 @@ class MainWindowBase(QMainWindow):
         if not os.path.isfile(gdsfile) or self.metals_list is None:
             return set()
         cellname = cellname_from_display(self.file_tab.cellname_box.currentText())
-        purpose_text = self.file_tab.purpose_edit.text().strip()
-        try:
-            purposelist = ast.literal_eval('[' + purpose_text + ']') if purpose_text else [0]
-        except Exception:
-            purposelist = [0]
+        purposelist = normalize_purpose_list(self.file_tab.purpose_edit.text())
 
         if _derived_layer_range_is_safe(self.metals_list, layer_min, layer_max):
             try:

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM/simplify_gds.py

@@ -19,16 +19,17 @@
 """
 simplify_gds.py
 
-Tools > Simplify GDS... : removes floating (unconnected) metal fill and/or
-fills in small cutouts on the currently loaded GDS file, writing the result
-to a new GDS file. Both operations come from gds_prepare_for_EM (a sibling
-package, already an editable install in this venv) and are called in-process
-- no subprocess/CLI involved.
-
-No technology-specific layer numbers are hardcoded here: the list of metal
-layers to process is derived entirely from the XML stackup already parsed
-into MainWindow.metals_list (gds2palace's stackup_reader), same as every
-other setupEM feature that needs to know "which GDS layers are metal".
+Tools > Simplify GDS... : removes floating (unconnected) metal fill, fills
+in small cutouts and/or merges via arrays on the currently loaded GDS file,
+writing the result to a new GDS file. All operations come from
+gds_prepare_for_EM (a sibling package, already an editable install in this
+venv) and are called in-process - no subprocess/CLI involved.
+
+No technology-specific layer numbers are hardcoded here: the metal layers to
+process, the via layers and the metal layers above/below each via are derived
+entirely from the XML stackup already parsed into MainWindow.metals_list
+(gds2palace's stackup_reader), same as every other setupEM feature that needs
+to know "which GDS layers are metal".
 """
 
 import os, io, contextlib, traceback, tempfile
@@ -130,7 +131,7 @@ def _flatten_cell(lib, cellname):
 def run_simplify(gds_path, metal_layers, output_path, cellname="",
                   do_cutouts=False, max_hole_area=None,
                   do_floating=False, fill_minsize=1.0, fill_maxsize=None, fill_mincount=20,
-                  do_merge=False):
+                  do_merge=False, via_layers=None, via_merge_size=0):
     """Load gds_path, optionally fill small cutouts, remove floating metal
     fill, and/or merge (boolean OR) polygons per layer as a final pass, on
     the given metal_layers, write the result to output_path. Mirrors the
@@ -139,12 +140,21 @@ def run_simplify(gds_path, metal_layers, output_path, cellname="",
     (needs a flattened, per-layer-merged cell first so that touching fill
     tiles aren't mistaken for isolated ones - see
     find_isolated_same_size_polygons_by_layer()'s own docstring), per-layer
-    merge last.
+    merge, then via array merging.
+
+    via_layers: list of (via layer, metal layers above, metal layers below),
+    GDS layer numbers. Vias closer than via_merge_size (microns) are merged
+    if they connect the same metal shapes above and below, see
+    gds_prepare_for_EM.merge_via_array_by_metal_overlap(). Vias without metal
+    above or below are kept unchanged. None or via_merge_size <= 0: no via
+    merging.
     """
     from gds_prepare_for_EM import (
         remove_cutout_keep_hierarchy,
         merge_polygons_by_layer,
         find_isolated_same_size_polygons_by_layer,
+        merge_polygons,
+        merge_via_array_by_metal_overlap,
     )
     from gds_geometry_utils import validate_and_repair_polygons
 
@@ -187,6 +197,31 @@ def run_simplify(gds_path, metal_layers, output_path, cellname="",
         lib, top_cell = _flatten_cell(lib, cellname)
         lib = merge_polygons_by_layer(top_cell, layers_list=metal_layers)
 
+    if via_layers and via_merge_size > 0:
+        lib, top_cell = _flatten_cell(lib, cellname)
+        lpp = top_cell.get_polygons(by_spec=True)
+        print(f'Via array merging (distance {via_merge_size} um):')
+
+        def metal_polygons(layers):
+            polygons = [p for (layer, purpose), polys in lpp.items() if layer in layers for p in polys]
+            # touching metal pieces are one metal shape for via grouping
+            return merge_polygons(polygons) if polygons else []
+
+        for via_layer, above_layers, below_layers in via_layers:
+            purposes = [purpose for (layer, purpose) in lpp if layer == via_layer]
+            if not purposes:
+                continue
+            above, below = metal_polygons(above_layers), metal_polygons(below_layers)
+            for purpose in purposes:
+                vias = lpp[(via_layer, purpose)]
+                merged = merge_via_array_by_metal_overlap(
+                    vias, above, below, via_merge_size, keep_unmatched=True)
+                top_cell.remove_polygons(
+                    lambda pts, layer, datatype: layer == via_layer and datatype == purpose)
+                for pts in merged:
+                    top_cell.add(gdspy.Polygon(pts, layer=via_layer, datatype=purpose))
+                print(f'  layer {via_layer}:{purpose}: {len(vias)} -> {len(merged)} polygons')
+
     # Final polygon validity check/repair - always runs, regardless of which
     # operations above were selected. Catches any polygon still geometrically
     # invalid (self-intersecting) no matter the reason - e.g. a cutout
@@ -235,6 +270,14 @@ class SimplifyGdsDialog(QDialog):
             int(m.layernum) for m in metals_list.getallplanarmetals()
             if not (port_layer_min <= int(m.layernum) <= port_layer_max)
         ) if metals_list is not None else []
+        # via layers with the metal layers above/below them, for via array merging
+        self._via_layers = [
+            (int(m.layernum),
+             [int(n.layernum) for n in m.above if n.is_metal],
+             [int(n.layernum) for n in m.below if n.is_metal])
+            for m in metals_list.metals
+            if m.is_via and not (port_layer_min <= int(m.layernum) <= port_layer_max)
+        ] if metals_list is not None else []
 
         layout = QVBoxLayout(self)
 
@@ -326,13 +369,40 @@ class SimplifyGdsDialog(QDialog):
 
         layout.addWidget(cutout_group)
 
+        # ---- Merge via arrays ----
+        via_group = QGroupBox("Merge via arrays")
+        via_group.setCheckable(True)
+        via_group.setChecked(False)
+        via_group.setToolTip(
+            "Vias closer than this distance are merged into one shape, but only if they connect "
+            "the same metal shapes above and below, so merging never shorts different metal "
+            "shapes. Via layers and the metal layers above/below them come from the XML stackup."
+        )
+        via_layout = QVBoxLayout(via_group)
+        self.via_group = via_group
+
+        via_size_row = QHBoxLayout()
+        via_size_row.addWidget(row_label("Distance (µm)"))
+        self.via_merge_size_edit = QLineEdit(str(get_preference(app_name, "merge_polygon_size", "0.5")))
+        self.via_merge_size_edit.setStyleSheet(_EDIT_STYLE)
+        via_size_row.addWidget(self.via_merge_size_edit)
+        via_size_row.addStretch(1)
+        via_layout.addLayout(via_size_row)
+
+        via_note = QLabel("Merged vias in the output file are treated as solid metal: fill factor "
+                          "correction needs the original vias, which are then no longer in the file. "
+                          "For accurate via resistance, merge vias in the model instead (via array "
+                          "merge distance > 0 with fill factor correction).")
+        via_note.setWordWrap(True)
+        via_layout.addWidget(via_note)
+
         # ---- Merge per layer ----
         # remembers the user's own choice while the checkbox is forced/greyed
         # out by "Remove floating (unconnected) metal" (see
         # _on_floating_group_toggled() below), so it's restored rather than
         # lost once that group is unchecked again
         self._merge_user_choice = get_preference_bool(app_name, "simplify_merge_per_layer", True)
-        self.merge_per_layer_checkbox = QCheckBox("Merge polygons per layer (final step)")
+        self.merge_per_layer_checkbox = QCheckBox("Merge polygons per layer")
         self.merge_per_layer_checkbox.setChecked(self._merge_user_choice)
         self.merge_per_layer_checkbox.setToolTip(
             "Boolean-OR touching/overlapping polygons on the same layer into the minimal "
@@ -347,6 +417,9 @@ class SimplifyGdsDialog(QDialog):
         floating_group.toggled.connect(self._on_floating_group_toggled)
         self._on_floating_group_toggled(floating_group.isChecked())
 
+        # after "Merge polygons per layer": via merging runs last, see run_simplify()
+        layout.addWidget(via_group)
+
         # ---- Log area ----
         self.log_area = QPlainTextEdit()
         self.log_area.setReadOnly(True)
@@ -437,7 +510,8 @@ class SimplifyGdsDialog(QDialog):
         do_floating = self.floating_group.isChecked()
         do_cutouts = self.cutout_group.isChecked()
         do_merge = self.merge_per_layer_checkbox.isChecked()
-        if not do_floating and not do_cutouts and not do_merge:
+        do_via_merge = self.via_group.isChecked()
+        if not do_floating and not do_cutouts and not do_merge and not do_via_merge:
             QMessageBox.warning(self, "Error", "Enable at least one operation")
             return
 
@@ -455,6 +529,11 @@ class SimplifyGdsDialog(QDialog):
             fill_mincount = int(mincount_text) if mincount_text else 20
             max_hole_area = _parse_optional_float(self.max_hole_area_edit.text(), "Max cutout area")
             excluded_layers = _parse_layer_list(self.excluded_layers_edit.text())
+            via_merge_size = 0
+            if do_via_merge:
+                via_merge_size = _parse_optional_float(self.via_merge_size_edit.text(), "Via merge distance")
+                if via_merge_size is None or via_merge_size <= 0:
+                    raise ValueError("'Via merge distance' must be a number > 0")
         except ValueError as e:
             QMessageBox.warning(self, "Error", str(e))
             return
@@ -489,7 +568,9 @@ class SimplifyGdsDialog(QDialog):
                     do_cutouts=do_cutouts, max_hole_area=max_hole_area,
                     do_floating=do_floating, fill_minsize=fill_minsize,
                     fill_maxsize=fill_maxsize, fill_mincount=fill_mincount,
-                    do_merge=do_merge)
+                    do_merge=do_merge,
+                    via_layers=[v for v in self._via_layers if v[0] not in excluded_layers],
+                    via_merge_size=via_merge_size)
         except (Exception, SystemExit):
             printed = captured_stdout.getvalue().strip()
             details = (printed + "\n\n" + traceback.format_exc()) if printed else traceback.format_exc()

setupem-0.11.1/src/setupEM.egg-info/PKG-INFO

@@ -0,0 +1,26 @@
+Metadata-Version: 2.4
+Name: setupEM
+Version: 0.11.1
+Summary: Python tool for configuration of gds2palace workflow with GUI.
+Author-email: Volker Muehlhaus <volker@muehlhaus.com>
+License-Expression: GPL-3.0-or-later
+Project-URL: Homepage, https://github.com/VolkerMuehlhaus/setupEM
+Project-URL: Repository, https://github.com/VolkerMuehlhaus/setupEM
+Project-URL: Changelog, https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: gds2palace>=0.8.0
+Requires-Dist: gds_prepare_for_EM>=1.3.0
+Requires-Dist: PySide6
+Requires-Dist: shiboken6
+Requires-Dist: scipy
+Requires-Dist: requests
+Requires-Dist: scikit-rf
+Requires-Dist: matplotlib
+Requires-Dist: numpy
+Requires-Dist: gdspy
+Requires-Dist: meshio
+Requires-Dist: pyvista
+Requires-Dist: pyvistaqt
+Dynamic: license-file

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM.egg-info/SOURCES.txt

@@ -1,6 +1,5 @@
 LICENSE
 README.md
-README_pypi.md
 pyproject.toml
 src/setupEM/__init__.py
 src/setupEM/__main__.py

{setupem-0.10.2 → setupem-0.11.1}/src/setupEM.egg-info/requires.txt

@@ -1,5 +1,5 @@
 gds2palace>=0.8.0
-gds_prepare_for_EM>=1.2.0
+gds_prepare_for_EM>=1.3.0
 PySide6
 shiboken6
 scipy

setupem-0.10.2/PKG-INFO

@@ -1,103 +0,0 @@
-Metadata-Version: 2.4
-Name: setupEM
-Version: 0.10.2
-Summary: Python tool for configuration of gds2palace workflow with GUI.
-Author-email: Volker Muehlhaus <volker@muehlhaus.com>
-License-Expression: GPL-3.0-or-later
-Project-URL: Homepage, https://github.com/VolkerMuehlhaus/setupEM
-Project-URL: Repository, https://github.com/VolkerMuehlhaus/setupEM
-Project-URL: Changelog, https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: gds2palace>=0.8.0
-Requires-Dist: gds_prepare_for_EM>=1.2.0
-Requires-Dist: PySide6
-Requires-Dist: shiboken6
-Requires-Dist: scipy
-Requires-Dist: requests
-Requires-Dist: scikit-rf
-Requires-Dist: matplotlib
-Requires-Dist: numpy
-Requires-Dist: gdspy
-Requires-Dist: meshio
-Requires-Dist: pyvista
-Requires-Dist: pyvistaqt
-Dynamic: license-file
-
-# Python GUI for gds2palace 
-
-![Intro](https://raw.githubusercontent.com/VolkerMuehlhaus/setupEM/main/doc/png/setupEM_banner.png)
-
-## Install
-
-    pip install setupEM
-
-**Full documentation, installation guide, and usage walkthrough:**
-https://github.com/VolkerMuehlhaus/setupEM
-
-## Recent changes
-
-# What's New - September 30, 2026
-
-The **Adaptive mesh refinement (AMR)** group on the Mesh and Boundaries tab is now called **Solver & Adaptive Mesh Refinement (AMR)** and has a new Palace linear solver setting, shown with **Show advanced configuration** = **Yes**. 
-
-**Complex coarse solve** (default **Yes** for every model, set in **Preferences > Palace**) lets Palace's direct coarse solver factorize the full complex system instead of only its real part. With **No** (Palace's own default), some models don't converge at some frequencies and get wrong S-parameters there: a D-band line failed at 170 GHz, and an inductor failed at 2.4 GHz with 1.1 nH instead of 2.5 nH, while it converged at 0.1 and 10 GHz. With **Yes** both converged in 1-31 iterations and ran 3.5-6x faster. Models that already converge give identical results in about the same or less time. The cost is peak RAM, depending on the model 1.0-1.6x at order 2 and 1.5-1.9x at order 1; the AMR RAM estimate includes this. 
-
-**Maximum solver iterations** (400) and **Solver tolerance** (1e-6) can now be changed too, in **Preferences > Palace**. These settings require gds2palace v0.8.0 or later and are hidden with an older version. setupEM module installation now requires gds2palace v0.8.0 or later, which also restores the dielectric loss tangent in Palace models that had been deleted by mistake.
-
-**Conformal AMR (experimental)** is a new advanced setting in the **Solver & Adaptive Mesh Refinement (AMR)** group (default **No**, set in **Preferences > Palace**). With AMR iterations > 0, it switches Palace from its default nonconformal (hanging-node) mesh refinement to conformal refinement (gds2palace `settings['adaptive_mesh_conformal']`). In the test cases so far it converged in fewer AMR iterations (D-band balun: 2 iterations instead of 4, in half the time), but the mesh cell count grows faster per iteration.
-
-setupEM now warns when Palace's linear solver does **not converge**: Palace carries on and writes S-parameters for that frequency anyway, but they are unreliable. Each case gets a ⚠ warning in the Log panel with its frequency, and all of them are listed again at the end of the run.
-
-# What's New - September 29, 2026
-
-The built-in **3D field viewer** now shows frequencies instead of bare numbers: the **Cycle** picker of a multi-frequency Palace field dump lists e.g. "6 GHz (cycle 1)", and Palace's extra error-indicator dump is listed as "geometry" right away. For Elmer (EM), each result file in the **Result File** picker shows its frequency, e.g. "fields_t0002.vtu - 7.5 GHz". The cycle number is kept in the label, so it still matches `field_viewer.py --cycle <N>`.
-
-# What's New - September 26, 2026
-
-**Result Viewer**: new frequency **Marker** that reads out all curves at the same frequency, shown on the plots and in a table below. Set it by clicking a plot, typing a frequency or using the Left/Right arrow keys; right-click a plot to jump to the (next) min/max.
-
-The **AMR maximum DOF** setting now shows an estimate of the RAM that Palace will need at that mesh size, both on the Mesh tab and in Preferences > Palace. The estimate is based on existing Palace results (about 12 GB per million DOF, up to 15 GB). On the Mesh tab, it turns into a warning when the worst case exceeds the **"Stop Palace if memory exceeds"** limit.
-
-**Stackup Preview**: three or more layers at the same height (e.g. resistor sheets on top of Activ) are now drawn side by side instead of on top of each other, via labels sit near the upper end of the via, and sheet resistance labels show the correct unit (e.g. RHIGH: Rs=1360 Ω, was shown as 1360000 mΩ).
-
-The bundled stackup files now include the latest parameterized gds2palace stackups for EM and thermal simulation: **SG13G2_FEM_200um.xml**, **SG13G2_FEM_200um_passi3D.xml** (conformal passivation around TopMetal2) and **SG13CMOS5L_200um.xml**. Chip and air height can be changed with the **Override stackup Variables** table. The previous SG13G2_100um.xml, SG13G2_200um.xml and SG13G2_nosub.xml are still included, so existing models keep working.
-
-# What's New - September 25, 2026
-
-Added a **Correction for via array cross section** option on the Input Files tab, below via array merging, in setupEM (Palace and Elmer) and setupThermal. Merging fills the gaps between vias with via material, which overestimates the conductivity of a via array; when enabled, the conductivity of each merged via polygon (heat conductivity for thermal models) is multiplied by its fill factor (original via area / merged polygon area). This option requires gds2palace v0.7.0 or later and is hidden with an older version, which would silently ignore it.
-
-# What's New - September 22-24, 2026
-
-Added a **Conductor meshing** option (Palace only) on the Mesh and Boundaries tab: **Surface impedance** (default, as before) or **Solve inside (volume mesh)**, which models conductors as solid bulk-conductivity volumes instead - more accurate at low frequency, at the cost of more RAM/simulation time and reduced accuracy at higher frequencies. This option requires gds2palace v0.6.0 or later, earlier version silently ignore this setting.  
-
-Better display in **Stackup Preview**'s for metals/vias that push outside their base dieelectric.  
-
-Palace's real memory usage is now measured directly from the running solver process(es) instead of parsed from its own log output, which could be inaccurate - this also makes the **"Stop Palace if memory exceeds"** kill switch more reliable.
-
-The built-in **3D field viewer** can now switch between the results of a multi-frequency Palace field-dump ("fdump") run: a new **Cycle** picker appears whenever the loaded result file has more than one solved frequency, and `field_viewer.py --cycle <N>` selects one from the command line. Previously the viewer could only ever show one fixed cycle of such a file, with no way to see the others.
-
-Added **File > New**, which resets setupEM/setupThermal to the same blank state as a freshly started application - useful for starting a new model without restarting the app.
-
-Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
-
----
-
-**Note:** the `setupEM` PyPI package itself requires:
-
-- gds2palace>=0.7.0
-- gds_prepare_for_EM>=1.2.0
-- PySide6
-- shiboken6
-- scipy
-- requests
-- scikit-rf
-- matplotlib
-- numpy
-- gdspy
-- meshio
-- pyvista
-- pyvistaqt
-
-(Other Python modules mentioned above are only needed to run standalone helper scripts in this repository, not to use the installed package.)

setupem-0.10.2/README_pypi.md

@@ -1,76 +0,0 @@
-# Python GUI for gds2palace 
-
-![Intro](https://raw.githubusercontent.com/VolkerMuehlhaus/setupEM/main/doc/png/setupEM_banner.png)
-
-## Install
-
-    pip install setupEM
-
-**Full documentation, installation guide, and usage walkthrough:**
-https://github.com/VolkerMuehlhaus/setupEM
-
-## Recent changes
-
-# What's New - September 30, 2026
-
-The **Adaptive mesh refinement (AMR)** group on the Mesh and Boundaries tab is now called **Solver & Adaptive Mesh Refinement (AMR)** and has a new Palace linear solver setting, shown with **Show advanced configuration** = **Yes**. 
-
-**Complex coarse solve** (default **Yes** for every model, set in **Preferences > Palace**) lets Palace's direct coarse solver factorize the full complex system instead of only its real part. With **No** (Palace's own default), some models don't converge at some frequencies and get wrong S-parameters there: a D-band line failed at 170 GHz, and an inductor failed at 2.4 GHz with 1.1 nH instead of 2.5 nH, while it converged at 0.1 and 10 GHz. With **Yes** both converged in 1-31 iterations and ran 3.5-6x faster. Models that already converge give identical results in about the same or less time. The cost is peak RAM, depending on the model 1.0-1.6x at order 2 and 1.5-1.9x at order 1; the AMR RAM estimate includes this. 
-
-**Maximum solver iterations** (400) and **Solver tolerance** (1e-6) can now be changed too, in **Preferences > Palace**. These settings require gds2palace v0.8.0 or later and are hidden with an older version. setupEM module installation now requires gds2palace v0.8.0 or later, which also restores the dielectric loss tangent in Palace models that had been deleted by mistake.
-
-**Conformal AMR (experimental)** is a new advanced setting in the **Solver & Adaptive Mesh Refinement (AMR)** group (default **No**, set in **Preferences > Palace**). With AMR iterations > 0, it switches Palace from its default nonconformal (hanging-node) mesh refinement to conformal refinement (gds2palace `settings['adaptive_mesh_conformal']`). In the test cases so far it converged in fewer AMR iterations (D-band balun: 2 iterations instead of 4, in half the time), but the mesh cell count grows faster per iteration.
-
-setupEM now warns when Palace's linear solver does **not converge**: Palace carries on and writes S-parameters for that frequency anyway, but they are unreliable. Each case gets a ⚠ warning in the Log panel with its frequency, and all of them are listed again at the end of the run.
-
-# What's New - September 29, 2026
-
-The built-in **3D field viewer** now shows frequencies instead of bare numbers: the **Cycle** picker of a multi-frequency Palace field dump lists e.g. "6 GHz (cycle 1)", and Palace's extra error-indicator dump is listed as "geometry" right away. For Elmer (EM), each result file in the **Result File** picker shows its frequency, e.g. "fields_t0002.vtu - 7.5 GHz". The cycle number is kept in the label, so it still matches `field_viewer.py --cycle <N>`.
-
-# What's New - September 26, 2026
-
-**Result Viewer**: new frequency **Marker** that reads out all curves at the same frequency, shown on the plots and in a table below. Set it by clicking a plot, typing a frequency or using the Left/Right arrow keys; right-click a plot to jump to the (next) min/max.
-
-The **AMR maximum DOF** setting now shows an estimate of the RAM that Palace will need at that mesh size, both on the Mesh tab and in Preferences > Palace. The estimate is based on existing Palace results (about 12 GB per million DOF, up to 15 GB). On the Mesh tab, it turns into a warning when the worst case exceeds the **"Stop Palace if memory exceeds"** limit.
-
-**Stackup Preview**: three or more layers at the same height (e.g. resistor sheets on top of Activ) are now drawn side by side instead of on top of each other, via labels sit near the upper end of the via, and sheet resistance labels show the correct unit (e.g. RHIGH: Rs=1360 Ω, was shown as 1360000 mΩ).
-
-The bundled stackup files now include the latest parameterized gds2palace stackups for EM and thermal simulation: **SG13G2_FEM_200um.xml**, **SG13G2_FEM_200um_passi3D.xml** (conformal passivation around TopMetal2) and **SG13CMOS5L_200um.xml**. Chip and air height can be changed with the **Override stackup Variables** table. The previous SG13G2_100um.xml, SG13G2_200um.xml and SG13G2_nosub.xml are still included, so existing models keep working.
-
-# What's New - September 25, 2026
-
-Added a **Correction for via array cross section** option on the Input Files tab, below via array merging, in setupEM (Palace and Elmer) and setupThermal. Merging fills the gaps between vias with via material, which overestimates the conductivity of a via array; when enabled, the conductivity of each merged via polygon (heat conductivity for thermal models) is multiplied by its fill factor (original via area / merged polygon area). This option requires gds2palace v0.7.0 or later and is hidden with an older version, which would silently ignore it.
-
-# What's New - September 22-24, 2026
-
-Added a **Conductor meshing** option (Palace only) on the Mesh and Boundaries tab: **Surface impedance** (default, as before) or **Solve inside (volume mesh)**, which models conductors as solid bulk-conductivity volumes instead - more accurate at low frequency, at the cost of more RAM/simulation time and reduced accuracy at higher frequencies. This option requires gds2palace v0.6.0 or later, earlier version silently ignore this setting.  
-
-Better display in **Stackup Preview**'s for metals/vias that push outside their base dieelectric.  
-
-Palace's real memory usage is now measured directly from the running solver process(es) instead of parsed from its own log output, which could be inaccurate - this also makes the **"Stop Palace if memory exceeds"** kill switch more reliable.
-
-The built-in **3D field viewer** can now switch between the results of a multi-frequency Palace field-dump ("fdump") run: a new **Cycle** picker appears whenever the loaded result file has more than one solved frequency, and `field_viewer.py --cycle <N>` selects one from the command line. Previously the viewer could only ever show one fixed cycle of such a file, with no way to see the others.
-
-Added **File > New**, which resets setupEM/setupThermal to the same blank state as a freshly started application - useful for starting a new model without restarting the app.
-
-Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
-
----
-
-**Note:** the `setupEM` PyPI package itself requires:
-
-- gds2palace>=0.7.0
-- gds_prepare_for_EM>=1.2.0
-- PySide6
-- shiboken6
-- scipy
-- requests
-- scikit-rf
-- matplotlib
-- numpy
-- gdspy
-- meshio
-- pyvista
-- pyvistaqt
-
-(Other Python modules mentioned above are only needed to run standalone helper scripts in this repository, not to use the installed package.)

setupem-0.10.2/src/setupEM.egg-info/PKG-INFO

@@ -1,103 +0,0 @@
-Metadata-Version: 2.4
-Name: setupEM
-Version: 0.10.2
-Summary: Python tool for configuration of gds2palace workflow with GUI.
-Author-email: Volker Muehlhaus <volker@muehlhaus.com>
-License-Expression: GPL-3.0-or-later
-Project-URL: Homepage, https://github.com/VolkerMuehlhaus/setupEM
-Project-URL: Repository, https://github.com/VolkerMuehlhaus/setupEM
-Project-URL: Changelog, https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md
-Requires-Python: >=3.9
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: gds2palace>=0.8.0
-Requires-Dist: gds_prepare_for_EM>=1.2.0
-Requires-Dist: PySide6
-Requires-Dist: shiboken6
-Requires-Dist: scipy
-Requires-Dist: requests
-Requires-Dist: scikit-rf
-Requires-Dist: matplotlib
-Requires-Dist: numpy
-Requires-Dist: gdspy
-Requires-Dist: meshio
-Requires-Dist: pyvista
-Requires-Dist: pyvistaqt
-Dynamic: license-file
-
-# Python GUI for gds2palace 
-
-![Intro](https://raw.githubusercontent.com/VolkerMuehlhaus/setupEM/main/doc/png/setupEM_banner.png)
-
-## Install
-
-    pip install setupEM
-
-**Full documentation, installation guide, and usage walkthrough:**
-https://github.com/VolkerMuehlhaus/setupEM
-
-## Recent changes
-
-# What's New - September 30, 2026
-
-The **Adaptive mesh refinement (AMR)** group on the Mesh and Boundaries tab is now called **Solver & Adaptive Mesh Refinement (AMR)** and has a new Palace linear solver setting, shown with **Show advanced configuration** = **Yes**. 
-
-**Complex coarse solve** (default **Yes** for every model, set in **Preferences > Palace**) lets Palace's direct coarse solver factorize the full complex system instead of only its real part. With **No** (Palace's own default), some models don't converge at some frequencies and get wrong S-parameters there: a D-band line failed at 170 GHz, and an inductor failed at 2.4 GHz with 1.1 nH instead of 2.5 nH, while it converged at 0.1 and 10 GHz. With **Yes** both converged in 1-31 iterations and ran 3.5-6x faster. Models that already converge give identical results in about the same or less time. The cost is peak RAM, depending on the model 1.0-1.6x at order 2 and 1.5-1.9x at order 1; the AMR RAM estimate includes this. 
-
-**Maximum solver iterations** (400) and **Solver tolerance** (1e-6) can now be changed too, in **Preferences > Palace**. These settings require gds2palace v0.8.0 or later and are hidden with an older version. setupEM module installation now requires gds2palace v0.8.0 or later, which also restores the dielectric loss tangent in Palace models that had been deleted by mistake.
-
-**Conformal AMR (experimental)** is a new advanced setting in the **Solver & Adaptive Mesh Refinement (AMR)** group (default **No**, set in **Preferences > Palace**). With AMR iterations > 0, it switches Palace from its default nonconformal (hanging-node) mesh refinement to conformal refinement (gds2palace `settings['adaptive_mesh_conformal']`). In the test cases so far it converged in fewer AMR iterations (D-band balun: 2 iterations instead of 4, in half the time), but the mesh cell count grows faster per iteration.
-
-setupEM now warns when Palace's linear solver does **not converge**: Palace carries on and writes S-parameters for that frequency anyway, but they are unreliable. Each case gets a ⚠ warning in the Log panel with its frequency, and all of them are listed again at the end of the run.
-
-# What's New - September 29, 2026
-
-The built-in **3D field viewer** now shows frequencies instead of bare numbers: the **Cycle** picker of a multi-frequency Palace field dump lists e.g. "6 GHz (cycle 1)", and Palace's extra error-indicator dump is listed as "geometry" right away. For Elmer (EM), each result file in the **Result File** picker shows its frequency, e.g. "fields_t0002.vtu - 7.5 GHz". The cycle number is kept in the label, so it still matches `field_viewer.py --cycle <N>`.
-
-# What's New - September 26, 2026
-
-**Result Viewer**: new frequency **Marker** that reads out all curves at the same frequency, shown on the plots and in a table below. Set it by clicking a plot, typing a frequency or using the Left/Right arrow keys; right-click a plot to jump to the (next) min/max.
-
-The **AMR maximum DOF** setting now shows an estimate of the RAM that Palace will need at that mesh size, both on the Mesh tab and in Preferences > Palace. The estimate is based on existing Palace results (about 12 GB per million DOF, up to 15 GB). On the Mesh tab, it turns into a warning when the worst case exceeds the **"Stop Palace if memory exceeds"** limit.
-
-**Stackup Preview**: three or more layers at the same height (e.g. resistor sheets on top of Activ) are now drawn side by side instead of on top of each other, via labels sit near the upper end of the via, and sheet resistance labels show the correct unit (e.g. RHIGH: Rs=1360 Ω, was shown as 1360000 mΩ).
-
-The bundled stackup files now include the latest parameterized gds2palace stackups for EM and thermal simulation: **SG13G2_FEM_200um.xml**, **SG13G2_FEM_200um_passi3D.xml** (conformal passivation around TopMetal2) and **SG13CMOS5L_200um.xml**. Chip and air height can be changed with the **Override stackup Variables** table. The previous SG13G2_100um.xml, SG13G2_200um.xml and SG13G2_nosub.xml are still included, so existing models keep working.
-
-# What's New - September 25, 2026
-
-Added a **Correction for via array cross section** option on the Input Files tab, below via array merging, in setupEM (Palace and Elmer) and setupThermal. Merging fills the gaps between vias with via material, which overestimates the conductivity of a via array; when enabled, the conductivity of each merged via polygon (heat conductivity for thermal models) is multiplied by its fill factor (original via area / merged polygon area). This option requires gds2palace v0.7.0 or later and is hidden with an older version, which would silently ignore it.
-
-# What's New - September 22-24, 2026
-
-Added a **Conductor meshing** option (Palace only) on the Mesh and Boundaries tab: **Surface impedance** (default, as before) or **Solve inside (volume mesh)**, which models conductors as solid bulk-conductivity volumes instead - more accurate at low frequency, at the cost of more RAM/simulation time and reduced accuracy at higher frequencies. This option requires gds2palace v0.6.0 or later, earlier version silently ignore this setting.  
-
-Better display in **Stackup Preview**'s for metals/vias that push outside their base dieelectric.  
-
-Palace's real memory usage is now measured directly from the running solver process(es) instead of parsed from its own log output, which could be inaccurate - this also makes the **"Stop Palace if memory exceeds"** kill switch more reliable.
-
-The built-in **3D field viewer** can now switch between the results of a multi-frequency Palace field-dump ("fdump") run: a new **Cycle** picker appears whenever the loaded result file has more than one solved frequency, and `field_viewer.py --cycle <N>` selects one from the command line. Previously the viewer could only ever show one fixed cycle of such a file, with no way to see the others.
-
-Added **File > New**, which resets setupEM/setupThermal to the same blank state as a freshly started application - useful for starting a new model without restarting the app.
-
-Full history: [CHANGES.md](https://github.com/VolkerMuehlhaus/setupEM/blob/main/doc/CHANGES.md)
-
----
-
-**Note:** the `setupEM` PyPI package itself requires:
-
-- gds2palace>=0.7.0
-- gds_prepare_for_EM>=1.2.0
-- PySide6
-- shiboken6
-- scipy
-- requests
-- scikit-rf
-- matplotlib
-- numpy
-- gdspy
-- meshio
-- pyvista
-- pyvistaqt
-
-(Other Python modules mentioned above are only needed to run standalone helper scripts in this repository, not to use the installed package.)