Added functions to aid junction tuning within cells

Junction data can be extracted from a given cell hierarchy,
both if the cell contains or doesn't contain PCell data.

This junction data can later be added into another cell
retaining junction position and orientation, with possibility
to tune junction parameters and junction type using external files.

klayout_package/python/kqcircuits/masks/mask_export.py

@@ -35,6 +35,7 @@
 from kqcircuits.util.geometry_json_encoder import GeometryJsonEncoder
 from kqcircuits.util.netlist_extraction import export_cell_netlist
 from kqcircuits.util.export_helper import export_drc_report
+from kqcircuits.util.replace_junctions import extract_junctions, get_tuned_junction_json
 
 
 def export_mask_set(mask_set, skip_extras=False):
@@ -67,6 +68,8 @@ def export_chip(chip_cell, chip_name, chip_dir, layout, export_drc, alt_netlists
     dummy_cell = layout.create_cell(chip_name)
     dummy_cell.insert(pya.DCellInstArray(chip_cell.cell_index(), pya.DTrans()))
     _export_cell(chip_dir / f"{chip_name}_with_pcells.oas", dummy_cell, "all")
+    if not skip_extras:
+        export_junction_parameters(dummy_cell, chip_dir / f"{chip_name}_junction_parameters.json")
     dummy_cell.delete()
     static_cell = layout.cell(layout.convert_cell_to_static(chip_cell.cell_index()))
 
@@ -383,3 +386,13 @@ def _get_directory(directory):
 
 def get_mask_layout_full_name(mask_set, mask_layout):
     return f"{mask_set.name}_v{mask_set.version}-{mask_layout.face_id}{mask_layout.extra_id}"
+
+
+def export_junction_parameters(cell, path):
+    """Exports a json file containing all parameter values for each junction in the given chip (as cell)"""
+    junctions = extract_junctions(cell, {})
+    if len(junctions) > 0:
+        params_json = json.dumps(get_tuned_junction_json(junctions), indent=2)
+        with open(path, 'w') as file:
+            file.write(params_json)
+        logging.info(f"Exported tunable junction parameters to {path}")

klayout_package/python/scripts/macros/export/export_junction_parameters.lym

@@ -0,0 +1,67 @@
+<?xml version="1.0" encoding="utf-8"?>
+<klayout-macro>
+ <description>Exports junctions parameters</description>
+ <version/>
+ <category>pymacros</category>
+ <prolog/>
+ <epilog/>
+ <doc/>
+ <autorun>false</autorun>
+ <autorun-early>false</autorun-early>
+ <priority>0</priority>
+ <shortcut/>
+ <show-in-menu>false</show-in-menu>
+ <group-name/>
+ <menu-path/>
+ <interpreter>python</interpreter>
+ <dsl-interpreter-name/>
+ <text># This code is part of KQCircuits
+# Copyright (C) 2024 IQM Finland Oy
+#
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+# License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+# warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program. If not, see
+# https://www.gnu.org/licenses/gpl-3.0.html.
+#
+# The software distribution should follow IQM trademark policy for open-source software
+# (meetiqm.com/developers/osstmpolicy). IQM welcomes contributions to the code. Please see our contribution agreements
+# for individuals (meetiqm.com/developers/clas/individual) and organizations (meetiqm.com/developers/clas/organization).
+
+
+"""Exports all current junnction parameter values for each junction in the PCell.
+
+Assumes that a single chip exists in the top cell, and it is a PCell.
+Results of this macro can be used to tune junctions for cells without PCell data.
+"""
+
+import json
+from kqcircuits.klayout_view import KLayoutView
+from kqcircuits.util.replace_junctions import extract_junctions, get_tuned_junction_json
+
+top_cell = KLayoutView(current=True).active_cell
+
+### Set file location, or leave empty to get tuned junction JSON in the output
+FILE_LOCATION = ""
+
+try:
+  junctions = extract_junctions(top_cell, {})
+  if len(junctions) &gt; 0:
+    json_str = json.dumps(get_tuned_junction_json(junctions), indent=2)
+
+    if FILE_LOCATION:
+      with open(FILE_LOCATION, 'w') as file:
+        file.write(json_str)
+        print(f"Wrote junction parameters to {FILE_LOCATION}")
+    else:
+      print(json_str)
+  else:
+    print("No junctions detected")
+except ValueError:
+  raise ValueError("For this macro to work, the active layout must contain a chip PCell, for which PCell parameters are present")
+</text>
+</klayout-macro>

klayout_package/python/scripts/macros/export/export_probepoints_json.lym

@@ -41,7 +41,7 @@ from kqcircuits.util.export_helper import generate_probepoints_json
 
 top_cell = KLayoutView(current=True).active_cell
 
-### Set file location, or leave empty to get probepoint JSON empty
+### Set file location, or leave empty to get probepoint JSON in the output
 FILE_LOCATION = ""
 ### Action
 # See API docs on how to best call generate_probepoints_json for your purposes

klayout_package/python/scripts/macros/export/export_tuned_junctions.lym

@@ -0,0 +1,91 @@
+<?xml version="1.0" encoding="utf-8"?>
+<klayout-macro>
+ <description>Exports junctions in given chip with tuned parameters</description>
+ <version/>
+ <category>pymacros</category>
+ <prolog/>
+ <epilog/>
+ <doc/>
+ <autorun>false</autorun>
+ <autorun-early>false</autorun-early>
+ <priority>0</priority>
+ <shortcut/>
+ <show-in-menu>false</show-in-menu>
+ <group-name/>
+ <menu-path/>
+ <interpreter>python</interpreter>
+ <dsl-interpreter-name/>
+ <text># This code is part of KQCircuits
+# Copyright (C) 2024 IQM Finland Oy
+#
+# This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+# License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+# warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along with this program. If not, see
+# https://www.gnu.org/licenses/gpl-3.0.html.
+#
+# The software distribution should follow IQM trademark policy for open-source software
+# (meetiqm.com/developers/osstmpolicy). IQM welcomes contributions to the code. Please see our contribution agreements
+# for individuals (meetiqm.com/developers/clas/individual) and organizations (meetiqm.com/developers/clas/organization).
+
+
+"""Exports junctions of a chip to a separate file. Parameters of individual junctions may be tuned.
+
+Assumes that a single chip exists in the top cell.
+Will export a new .oas file in TMP path containing junctions of original cell,
+with possibly tuned junction parameters, and a "base_metal_gap" layer for reference.
+This new layout will also be opened in current KLayout session in new layout.
+Macro can be used on cells with or without PCell data.
+In the latter case the `tuned_junction_parameters` must include a value for every
+junction parameter of every junction in the cell.
+You can use "export_junction_parameters" macro on a PCell to get full listing of parameters,
+to later reuse on cells without PCell data.
+
+See kqcircuits.util.replace_junctions API docs for more technical details.
+"""
+
+import json
+from kqcircuits.defaults import TMP_PATH
+from kqcircuits.klayout_view import KLayoutView
+from kqcircuits.pya_resolver import pya
+from kqcircuits.util.replace_junctions import extract_junctions, place_junctions, copy_one_layer_of_cell
+
+top_cell = KLayoutView(current=True).active_cell
+
+# If there are too many parameters to tune (for example tuning junctions for file without PCells),
+# these can be written in a separate .json file and read from the macro
+EXTERNAL_TUNE_FILE = ""
+
+if EXTERNAL_TUNE_FILE:
+  with open(EXTERNAL_TUNE_FILE) as f:
+    tuned_junction_parameters = json.load(f)
+else:
+  # Or tuned parameters can be typed up here by hand
+  tuned_junction_parameters = {}
+  # Example: exaggerate junction width for qubit "qb_1" for "Single Xmons" PCell
+  # tuned_junction_parameters = {"qb_1": {"squid": {"junction_width": 2.0}}}
+
+junctions = extract_junctions(top_cell, tuned_junction_parameters)
+clean_cell_name = top_cell.basic_name().replace(" ", "").replace("*", "").split("$")[0]
+exported_file = str(TMP_PATH / f'tuned_junctions_{clean_cell_name}.oas')
+copy_one_layer_of_cell(exported_file, top_cell, junctions, "base_metal_gap")
+
+print(f"Extracted and tuned {len(junctions)} junctions")
+new_view = KLayoutView()
+new_view.layout.clear()
+new_view.layout.read(exported_file)
+top_cell = new_view.layout.top_cells()[-1]
+top_cell.flatten(True)
+place_junctions(top_cell, junctions)
+new_view.focus(top_cell)
+
+print(f"Saving tuned junctions to {exported_file}")
+svopt = pya.SaveLayoutOptions()
+svopt.set_format_from_filename(exported_file)
+new_view.layout.write(exported_file, svopt)
+</text>
+</klayout-macro>