waveorder 3.0.0a2__py3-none-any.whl → 3.0.0a3__py3-none-any.whl

waveorder/plugin/tab_recon.py

@@ -1,12 +1,24 @@
 import datetime
 import json
+import logging
 import os
 import threading
 import time
+import types
 import uuid
 import warnings
 from pathlib import Path
-from typing import TYPE_CHECKING, Annotated, Final, List, Literal, Union
+from typing import (
+    TYPE_CHECKING,
+    Annotated,
+    Any,
+    Final,
+    List,
+    Literal,
+    Union,
+    get_args,
+    get_origin,
+)
 
 from iohub.ngff import open_ome_zarr
 from magicgui import widgets
@@ -28,7 +40,8 @@ if TYPE_CHECKING:
 
 from concurrent.futures import ThreadPoolExecutor
 
-from pydantic.v1 import BaseModel, NonNegativeInt, ValidationError
+from pydantic import BaseModel, NonNegativeInt, ValidationError
+from pydantic_core import PydanticUndefinedType
 
 from waveorder.cli.settings import (
     BirefringenceApplyInverseSettings,
@@ -57,11 +70,11 @@ from waveorder.io import utils
 
 MSG_SUCCESS = {"msg": "success"}
 
-_validate_alert = "⚠"
-_validate_ok = "✔️"
+_validate_alert = "⚠️"
+_validate_ok = "✅"
 _green_dot = "🟢"
 _red_dot = "🔴"
-_info_icon = "ⓘ"
+_info_icon = "ℹ️"
 
 # For now replicate CLI processing modes - these could reside in the CLI settings file as well
 # for consistency
@@ -84,6 +97,48 @@ MULTI_JOBS_REFS = {}
 ROW_POP_QUEUE = []
 
 
+def unwrap_optional(ftype: Any) -> Any:
+    """Unwrap Optional[X] to get X. Handles both Optional[X] and X | None syntax.
+
+    Args:
+        ftype: A type annotation
+
+    Returns:
+        The unwrapped type, or ftype unchanged if not Optional
+    """
+    origin = get_origin(ftype)
+    if origin is Union or isinstance(ftype, types.UnionType):
+        args = [a for a in get_args(ftype) if a is not type(None)]
+        if len(args) == 1:
+            return args[0]
+    return ftype
+
+
+def is_subclass_of(
+    ftype: Any,
+    base: type | tuple[type, ...],
+    *,
+    require_optional: bool = False,
+) -> bool:
+    """Check if ftype (possibly Optional-wrapped) is a subclass of base.
+
+    Args:
+        ftype: A type annotation
+        base: The base type(s) to check against (can be tuple for multiple)
+        require_optional: If True, only return True if ftype was Optional-wrapped
+
+    Returns:
+        True if the (unwrapped) ftype is a subclass of base
+    """
+    inner = unwrap_optional(ftype)
+    if require_optional and inner is ftype:
+        return False
+    # Handle Annotated types by unwrapping them
+    if get_origin(inner) is Annotated:
+        inner = get_args(inner)[0]
+    return isinstance(inner, type) and issubclass(inner, base)
+
+
 # Main class for the Reconstruction tab
 # Not efficient since instantiated from GUI
 # Does not have access to common functions in main_widget
@@ -405,7 +460,9 @@ class Ui_ReconTab_Form(QWidget):
 
     def hideEvent(self, event):
         if event.type() == QEvent.Type.Hide and (
-            self._ui is not None and self._ui.isVisible()
+            hasattr(self, "_ui")
+            and self._ui is not None
+            and self._ui.isVisible()
         ):
             pass
 
@@ -1027,7 +1084,8 @@ class Ui_ReconTab_Form(QWidget):
                 json_txt = str(json_txt)
                 # ToDo: format it better
                 # formatted txt does not show up properly in msg-box ??
-            except:
+            except (TypeError, KeyError, AttributeError):
+                # msg is not in expected validation error format
                 json_txt = str(msg)
 
             # show is a message box
@@ -1305,26 +1363,15 @@ class Ui_ReconTab_Form(QWidget):
         except Exception as exc:
             return None, exc.args
 
-    # ToDo: Temporary fix to over ride the 'input_channel_names' default value
-    # Needs revisitation
     def fix_model(self, model, exclude_modes, attr_key, attr_val):
+        """Update model attribute while excluding specified modes."""
         try:
-            for mode in exclude_modes:
-                model = settings.ReconstructionSettings.copy(
-                    model,
-                    exclude={mode},
-                    deep=True,
-                    update={attr_key: attr_val},
-                )
-            settings.ReconstructionSettings.__setattr__(
-                model, attr_key, attr_val
-            )
-            if hasattr(model, attr_key):
-                model.__fields__[attr_key].default = attr_val
-                model.__fields__[attr_key].field_info.default = attr_val
-        except Exception as exc:
-            return print(exc.args)
-        return model
+            data = model.model_dump(exclude=set(exclude_modes))
+            data[attr_key] = attr_val
+            return settings.ReconstructionSettings.model_validate(data)
+        except ValidationError as exc:
+            logging.error(f"fix_model failed: {exc}")
+            return None
 
     # Creates UI controls from model based on selections
     def build_acq_contols(self):
@@ -2409,8 +2456,10 @@ class Ui_ReconTab_Form(QWidget):
         # instantiate the pydantic model form the kwargs we just pulled
         try:
             try:
-                pydantic_model = settings.ReconstructionSettings.parse_obj(
-                    pydantic_kwargs
+                pydantic_model = (
+                    settings.ReconstructionSettings.model_validate(
+                        pydantic_kwargs
+                    )
                 )
                 return pydantic_model, MSG_SUCCESS
             except ValidationError as exc:
@@ -2421,7 +2470,7 @@ class Ui_ReconTab_Form(QWidget):
     # test to make sure model converts to json which should ensure compatibility with yaml export
     def validate_and_return_json(self, pydantic_model):
         try:
-            json_format = pydantic_model.json(indent=4)
+            json_format = pydantic_model.model_dump_json(indent=4)
             return json_format, MSG_SUCCESS
         except Exception as exc:
             return None, exc.args
@@ -2465,47 +2514,62 @@ class Ui_ReconTab_Form(QWidget):
     # Ignoring NoneType since those should be Optional but maybe needs displaying ??
     # ToDo: Needs revisitation, Union check
     # Displaying Union field "time_indices" as LineEdit component
-    # excludes handles fields that are not supposed to show up from __fields__
+    # excludes handles fields that are not supposed to show up from model_fields
     # json_dict adds ability to provide new set of default values at time of container creation
 
     def add_pydantic_to_container(
         self,
-        py_model: Union[BaseModel, BaseModel],
+        py_model: type[BaseModel] | BaseModel,
         container: widgets.Container,
-        excludes=[],
+        excludes=None,
         json_dict=None,
     ):
         # recursively traverse a pydantic model adding widgets to a container. When a nested
         # pydantic model is encountered, add a new nested container
+        if excludes is None:
+            excludes = []
 
-        for field, field_def in py_model.__fields__.items():
+        # Access model_fields from the class, not the instance
+        model_class = (
+            py_model if isinstance(py_model, type) else type(py_model)
+        )
+        is_instance = not isinstance(py_model, type)
+        for field, field_def in model_class.model_fields.items():
             if field_def is not None and field not in excludes:
-                def_val = field_def.default
-                ftype = field_def.type_
-                toolTip = ""
-                try:
-                    for f_val in field_def.class_validators.keys():
-                        toolTip = f"{toolTip}{f_val} "
-                except Exception as e:
-                    pass
+                # Get actual instance value if py_model is an instance, otherwise use class default
+                if is_instance:
+                    def_val = getattr(py_model, field)
+                else:
+                    def_val = field_def.default
+                    if isinstance(def_val, PydanticUndefinedType):
+                        def_val = None
+                ftype = field_def.annotation
+
+                # Build tooltip from field metadata
+                tooltip_parts = []
+                if field_def.description:
+                    tooltip_parts.append(field_def.description)
+                if field_def.metadata:
+                    constraints = [str(m) for m in field_def.metadata]
+                    tooltip_parts.extend(constraints)
+                toolTip = " | ".join(tooltip_parts)
+                # Handle nested Pydantic models, including Optional[Model]
                 if (
-                    isinstance(ftype, BaseModel)
+                    is_subclass_of(ftype, BaseModel)
                     or ftype in PYDANTIC_CLASSES_DEF
                 ):
                     json_val = None
-                    if json_dict is not None:
+                    if json_dict is not None and field in json_dict:
                         json_val = json_dict[field]
                     # the field is a pydantic class, add a container for it and fill it
                     new_widget_cls = widgets.Container
-                    new_widget = new_widget_cls(name=field_def.name)
+                    new_widget = new_widget_cls(name=field)
                     new_widget.tooltip = toolTip
+                    # Unwrap Optional[Model] to get Model before recursing
+                    unwrapped_ftype = unwrap_optional(ftype)
                     self.add_pydantic_to_container(
-                        ftype, new_widget, excludes, json_val
+                        unwrapped_ftype, new_widget, excludes, json_val
                     )
-                # ToDo: Implement Union check, tried:
-                # pydantic.typing.is_union(ftype)
-                # isinstance(ftype, types.UnionType)
-                # https://stackoverflow.com/questions/45957615/how-to-check-a-variable-against-union-type-during-runtime
                 elif isinstance(ftype, type(Union[NonNegativeInt, List, str])):
                     if (
                         field == "background_path"
@@ -2534,31 +2598,53 @@ class Ui_ReconTab_Form(QWidget):
                         warnings.warn(
                             message=f"magicgui could not identify a widget for {py_model}.{field}, which has type {ftype}"
                         )
-                elif isinstance(def_val, float):
-                    # parse the field, add appropriate widget
-                    def_step_size = 0.001
-                    if field_def.name == "regularization_strength":
-                        def_step_size = 0.00001
-                    if def_val > -1 and def_val < 1:
+                elif isinstance(def_val, float) or (
+                    def_val is None
+                    and is_subclass_of(
+                        ftype, (int, float), require_optional=True
+                    )
+                ):
+                    # Handle float fields, including Optional[float] with None value
+
+                    # For Optional numeric types with None, use LineEdit instead of FloatSpinBox
+                    # This allows empty string to represent None
+                    # Note: if we entered via the is_subclass_of check, def_val is guaranteed None
+                    if def_val is None:
                         new_widget_cls, ops = get_widget_class(
                             None,
-                            ftype,
-                            dict(
-                                name=field_def.name,
-                                value=def_val,
-                                step=float(def_step_size),
-                            ),
+                            str,
+                            dict(name=field, value=""),
                         )
                         new_widget = new_widget_cls(**ops)
-                        new_widget.tooltip = toolTip
-                    else:
-                        new_widget_cls, ops = get_widget_class(
-                            None,
-                            ftype,
-                            dict(name=field_def.name, value=def_val),
+                        new_widget.tooltip = (
+                            toolTip + " (Optional - leave empty for None)"
                         )
-                        new_widget = new_widget_cls(**ops)
-                        new_widget.tooltip = toolTip
+                    else:
+                        # Regular float field
+                        def_step_size = 0.001
+                        if field == "regularization_strength":
+                            def_step_size = 0.00001
+
+                        if def_val > -1 and def_val < 1:
+                            new_widget_cls, ops = get_widget_class(
+                                None,
+                                ftype,
+                                dict(
+                                    name=field,
+                                    value=def_val,
+                                    step=float(def_step_size),
+                                ),
+                            )
+                            new_widget = new_widget_cls(**ops)
+                            new_widget.tooltip = toolTip
+                        else:
+                            new_widget_cls, ops = get_widget_class(
+                                None,
+                                ftype,
+                                dict(name=field, value=def_val),
+                            )
+                            new_widget = new_widget_cls(**ops)
+                            new_widget.tooltip = toolTip
                     if isinstance(new_widget, widgets.EmptyWidget):
                         warnings.warn(
                             message=f"magicgui could not identify a widget for {py_model}.{field}, which has type {ftype}"
@@ -2566,7 +2652,7 @@ class Ui_ReconTab_Form(QWidget):
                 else:
                     # parse the field, add appropriate widget
                     new_widget_cls, ops = get_widget_class(
-                        None, ftype, dict(name=field_def.name, value=def_val)
+                        None, ftype, dict(name=field, value=def_val)
                     )
                     new_widget = new_widget_cls(**ops)
                     if isinstance(new_widget, widgets.EmptyWidget):
@@ -2605,38 +2691,52 @@ class Ui_ReconTab_Form(QWidget):
         container: widgets.Container,
         pydantic_model,
         pydantic_kwargs: dict,
-        excludes=[],
+        excludes=None,
         json_dict=None,
     ):
         # given a container that was instantiated from a pydantic model, get the arguments
         # needed to instantiate that pydantic model from the container.
         # traverse model fields, pull out values from container
-        for field, field_def in pydantic_model.__fields__.items():
-            if field_def is not None and field not in excludes:
-                ftype = field_def.type_
-                if (
-                    isinstance(ftype, BaseModel)
-                    or ftype in PYDANTIC_CLASSES_DEF
-                ):
-                    # go deeper
-                    pydantic_kwargs[field] = (
-                        {}
-                    )  # new dictionary for the new nest level
-                    # any pydantic class will be a container, so pull that out to pass
-                    # to the recursive call
-                    sub_container = getattr(container, field_def.name)
-                    self.get_pydantic_kwargs(
-                        sub_container,
-                        ftype,
-                        pydantic_kwargs[field],
-                        excludes,
-                        json_dict,
-                    )
-                else:
-                    # not a pydantic class, just pull the field value from the container
-                    if hasattr(container, field_def.name):
-                        value = getattr(container, field_def.name).value
-                        pydantic_kwargs[field] = value
+        if excludes is None:
+            excludes = []
+
+        # Access model_fields from the class, not the instance
+        model_class = (
+            pydantic_model
+            if isinstance(pydantic_model, type)
+            else type(pydantic_model)
+        )
+
+        for field, field_def in model_class.model_fields.items():
+            if field in excludes:
+                continue
+
+            ftype = field_def.annotation
+            if is_subclass_of(ftype, BaseModel):
+                # Nested Pydantic model - recurse
+                pydantic_kwargs[field] = {}
+                self.get_pydantic_kwargs(
+                    getattr(container, field),
+                    unwrap_optional(ftype),
+                    pydantic_kwargs[field],
+                    excludes,
+                    json_dict,
+                )
+            else:
+                # Leaf field - extract value from container widget
+                value = getattr(container, field).value
+                # Handle Optional numeric types: convert empty string to None, parse numeric strings
+                if is_subclass_of(
+                    ftype, (int, float), require_optional=True
+                ) and isinstance(value, str):
+                    if value == "" or value.lower() in ("none", "null"):
+                        value = None
+                    else:
+                        try:
+                            value = float(value)
+                        except (ValueError, TypeError):
+                            pass
+                pydantic_kwargs[field] = value
 
     # copied from main_widget
     # file open/select dialog

{waveorder-3.0.0a2.dist-info → waveorder-3.0.0a3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: waveorder
-Version: 3.0.0a2
+Version: 3.0.0a3
 Summary: Wave-optical simulations and deconvolution of optical properties
 Author-email: CZ Biohub SF <compmicro@czbiohub.org>
 Maintainer-email: Talon Chandler <talon.chandler@czbiohub.org>, Shalin Mehta <shalin.mehta@czbiohub.org>
@@ -33,6 +33,18 @@ License: BSD 3-Clause License
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
         
+        ## License Notice for Dependencies
+        
+        This repository is licensed under the BSD License; however, it relies on certain 
+        third-party dependencies that are licensed under the GNU General Public License 
+        (GPL). Specifically:
+        
+        - PyQt5 is licensed under the GNU General Public License v3 or later (GPLv3+).
+        This library is not included in this repository but must be installed separately
+        by users. Please be aware that the GPL license terms apply to these 
+        dependencies, and certain uses of GPL-licensed code may have licensing 
+        implications for your own software.
+        
 Project-URL: Homepage, https://github.com/mehta-lab/waveorder
 Project-URL: Repository, https://github.com/mehta-lab/waveorder
 Project-URL: Issues, https://github.com/mehta-lab/waveorder/issues
@@ -71,14 +83,17 @@ Requires-Dist: qtpy
 Requires-Dist: wget>=3.2
 Provides-Extra: visual
 Requires-Dist: napari[pyqt6]; extra == "visual"
+Requires-Dist: PyQt6<6.8,>=6.5; extra == "visual"
 Requires-Dist: napari-ome-zarr>=0.3.2; extra == "visual"
 Requires-Dist: pycromanager==0.27.2; extra == "visual"
 Requires-Dist: jupyter; extra == "visual"
+Requires-Dist: jupytext; extra == "visual"
 Provides-Extra: dev
 Requires-Dist: black==25.1.0; extra == "dev"
 Requires-Dist: click>=8.2.0; extra == "dev"
 Requires-Dist: hypothesis; extra == "dev"
 Requires-Dist: napari[pyqt6]; extra == "dev"
+Requires-Dist: PyQt6<6.8,>=6.5; extra == "dev"
 Requires-Dist: pre-commit; extra == "dev"
 Requires-Dist: pytest-cov; extra == "dev"
 Requires-Dist: pytest-qt; extra == "dev"
@@ -102,7 +117,7 @@ Requires-Dist: waveorder[docs]; extra == "all"
 Dynamic: license-file
 
 <p align="center">
-  <img src="https://github.com/user-attachments/assets/1b4fabd4-2ead-40fa-ae88-99642a1589f1" alt="Image" width="50%">
+  <img src="https://github.com/user-attachments/assets/00367e51-0e0a-445e-8d12-2a273f9014aa" alt="Image" width="50%">
 </p>
 
 [![Python package index](https://img.shields.io/pypi/v/waveorder.svg)](https://pypi.org/project/waveorder)
@@ -313,7 +328,7 @@ We also maintain three dependency sets for different interfaces:
 
 ```sh
 pip install waveorder          # API, CLI
-pip install waveorder[visual]  # API, CLI, GUI  
+pip install waveorder[visual]  # API, CLI, GUI
 pip install waveorder[all]     # API, CLI, GUI, docs, dev dependencies
 ```
 

{waveorder-3.0.0a2.dist-info → waveorder-3.0.0a3.dist-info}/RECORD

@@ -1,9 +1,9 @@
 waveorder/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-waveorder/_version.py,sha256=4T3YnpoBezB_PnD8TGrripaPhzvljf62vnxX5xRPzJY,712
+waveorder/_version.py,sha256=1X31aM0jCGJPnD5p_rYNKOtonoGoP_xWzwERdd1UV5s,712
 waveorder/background_estimator.py,sha256=GFy3N0qqp5M6JVZBbIUvTYhSin8Njg7zA2WN69pKLAE,12398
 waveorder/correction.py,sha256=uAWDKXq-FYwi1obxxWq0A-suNVf1cvqUnPsDC-LIlsM,3460
 waveorder/filter.py,sha256=UatcxE3xqwwB1p0IVoEjH8Qw0CB6hvcXvnRR6IRNXsQ,7325
-waveorder/focus.py,sha256=hreENdCZCKj2pXoom3FgcevJX63q7-kKhCI9atRarcI,7956
+waveorder/focus.py,sha256=4IenjsMfwDkZlSImNMB3mnyuDz4XF7VJWiaCmzDLseI,10928
 waveorder/napari.yaml,sha256=iqmzGwSopu-L38yxuAnhMTuBvDqKIm2mTWfxjn6Duks,1463
 waveorder/optics.py,sha256=RikR3kkPFoVUS86jiGQZey7Jtz5Ga-xKWnXsexo3Okc,44242
 waveorder/reconstruct.py,sha256=nF00-uxYF67QVcNClp1VIB31ElUfbjO3RNxbxc0ELH4,832
@@ -14,44 +14,43 @@ waveorder/waveorder_reconstructor.py,sha256=-MluWmnZnCZm7Xu-8V8QWX9ma0_5oAZO2Xly
 waveorder/waveorder_simulator.py,sha256=uRRX_wcWzJzlVcfToLpIlh4e8Xt9NjTvdonyGEf2Z1c,45805
 waveorder/acq/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 waveorder/acq/acq_functions.py,sha256=4GJCkxncFunsRbLesf1LErY7CaA26dMh2goVVUr72y0,5128
-waveorder/acq/acquisition_workers.py,sha256=J30-ZdOej-R2jHnL5Nrwom3EV2xpnBYPGnJKsIyy-YA,22719
 waveorder/assets/HSV_legend.png,sha256=7k9l23V-is7TIVnKchIat9JE_UGSqjbRzgVROeNrNJU,12132
 waveorder/assets/JCh_legend.png,sha256=waQ980-7-APUqzuvBjKh5PKE91jaCbKire0NJf-y6AQ,14900
-waveorder/assets/waveorder_plugin_logo.png,sha256=euszlEwFVBBwLNpPm0WBwZob2YfJ0_9L4tznOxnbKuw,13817
+waveorder/assets/waveorder_plugin_logo.png,sha256=3advwUtIqhXJmHrqXF3NmWB8OMjQP2N-Nsbi-IaIQw8,14686
 waveorder/calib/Calibration.py,sha256=Fl6zQOJg4V6nKtbAlNL7s9kslmrxk6q-LAueh59F1bA,52007
 waveorder/calib/Optimization.py,sha256=uBQRvZ3tsG52pOSwnRj3Lduf_wVTTYfcjegAZsN58UE,13909
 waveorder/calib/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 waveorder/calib/calibration_workers.py,sha256=xI1Zg_D6m1wuls4af0Nlzl_3fADeAeHzSO2gWKGaORo,15325
-waveorder/cli/apply_inverse_models.py,sha256=L620cFSocqi9JlIT-EWSikbS9PcDOismH5zG6tgEmRA,10166
-waveorder/cli/apply_inverse_transfer_function.py,sha256=bFFa_zKUFd425jEF9LgRkDDb_2q9ZiljWFuGAQ45Zy0,13336
-waveorder/cli/compute_transfer_function.py,sha256=37ixvtrFsl7c9CIrjkDFg-XbWFENnHzB8J7UVy2EJpM,14253
+waveorder/cli/apply_inverse_models.py,sha256=8nrwj4bgHnha59uOvvV0PqdRyjyldWfUs_ZbfdtJ-ZE,10344
+waveorder/cli/apply_inverse_transfer_function.py,sha256=EgmzIoDX4o7GqYIQfk7wgJZ8DxqfXeTAJjDXbMOqWPY,13369
+waveorder/cli/compute_transfer_function.py,sha256=IfOtxVSYqcF9urDBxDftm8Txw3h6jNzAswIOgnXtRf0,14319
 waveorder/cli/gui_widget.py,sha256=bPbeAAQEFzD2WnlO_vKZ5RSdaFi6J3Psouzfuj7u9f4,1343
 waveorder/cli/main.py,sha256=uW18kwZOpYbgUKfGXexIF3LITxkUJeRMHnTmAwAPWjc,942
 waveorder/cli/monitor.py,sha256=XBhqyd7dxnXrfca23rm0oAILEnx8lEVPsS2oSfmt8kw,4757
 waveorder/cli/option_eat_all.py,sha256=GJgI4owf59IhZTtQiLsUy19WQJLJDXB-Gg7WIf5aREw,1823
 waveorder/cli/parsing.py,sha256=IWSjRCp2KQiEzw4T_aCvMSoPrKoRRbIJP0Tc8Pcb-R4,3476
-waveorder/cli/printing.py,sha256=rfGeONEsQT9AJnFY2VDCmi-1E62xdqwrwpJYBT_hFWg,237
+waveorder/cli/printing.py,sha256=tCWRE7YnE4ByROAhaYlCjJLnCwZ3IEcm3Bo6ZoO1uxI,326
 waveorder/cli/reconstruct.py,sha256=qbFCoMZC9utDofx8oU0BUljMC-MoN_ykrp1sXGe39zo,1792
-waveorder/cli/settings.py,sha256=J0CD_ZEv64ehe1WXgdsg9PQCrpim_tF1Uj0VsgE22kY,6418
-waveorder/cli/utils.py,sha256=r--7VDF_YiyjHx2ApI0tCf8CX076kpBzXR7OdzFbXwc,5646
+waveorder/cli/settings.py,sha256=d5EmqnzNjwDHVnP4xONAamBe6I4rdNHWS1pUXKyu1bw,6604
+waveorder/cli/utils.py,sha256=-7RYPUEzhTPhmgQUSptNxE1GmnAjzuucixEBWcRL0KI,5667
 waveorder/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 waveorder/io/_reader.py,sha256=l17s_-1aARCFn76VIpDljoOIL088uPx3A1mTl3T5l9o,1630
 waveorder/io/core_functions.py,sha256=g4HrkfcQinEhCPdt0FtRSXRXUjRL1ZQe5g0sClnjVZA,6553
 waveorder/io/metadata_reader.py,sha256=DiVqdJiwSduHa6eOrfJfcky1ZoFI3ySPEXJrbuFM8fg,5483
-waveorder/io/utils.py,sha256=0k4Co1CsCszJGG-t5xKmY2ZOZ5qDHI0XUA97Fpj9zNo,4732
+waveorder/io/utils.py,sha256=ArmKCq5_Wj3tyiD9Zl6jaUkjgIslJffJj5xRUGtMcMM,4804
 waveorder/io/visualization.py,sha256=u_EGSc2s1pkB-xvGVxmmMr2zQObihjkV0PCB_7yizak,4753
 waveorder/models/inplane_oriented_thick_pol3d.py,sha256=bx5yViNz7wY5BBXUea1Tw0RhYsEzErENRnAbgpa34C0,5992
 waveorder/models/inplane_oriented_thick_pol3d_vector.py,sha256=Qh1E0fWHh6KThQnW3TYBGmDtNrO98n9W42t6G_nQO5w,9759
 waveorder/models/isotropic_fluorescent_thick_3d.py,sha256=0bu9OdYj2aP1phzRxod8tExURaYdgwddAD61BbGF-lg,10387
 waveorder/models/isotropic_fluorescent_thin_3d.py,sha256=uOxRTOKu5Viv_KTKlW7c91M7hREx3eER-owKFyrhRCQ,10239
 waveorder/models/isotropic_thin_3d.py,sha256=BPp0DR3Pu8b7NpnGXUJ1ZqdGbs_P7-H5iVGagVClPtg,11328
-waveorder/models/phase_thick_3d.py,sha256=sOHphv6_SfarLxrhj4bcZwM-5bdjXS4-j6RCreOBTmA,8654
+waveorder/models/phase_thick_3d.py,sha256=eUmf_AbSDMwFNDfE8WPGr5sJShvL4YAjsZff_KO559k,12323
 waveorder/plugin/__init__.py,sha256=4Idw8HLl6LZ-E0cgW9mSsCAQk-D4Hnmoi0W9iaV6yrw,333
-waveorder/plugin/gui.py,sha256=b_5CdovGO7LF8qQNY9YJV4y1Gc_jEpYpVQ6mV0gJ1IM,80655
-waveorder/plugin/gui.ui,sha256=NjbgLSgYnLVs-OHeEmm224p0MNdT5kat3BrioA4jnCY,79154
+waveorder/plugin/gui.py,sha256=NazopP-wb3Fup4FWfgH4zWdkOKvilpxWrOXgsI0xquI,50593
+waveorder/plugin/gui.ui,sha256=7_CUDI2Wqbh2EBal9-ZmNJcb7cCCxiZcQe-DO6NBnM4,49920
 waveorder/plugin/job_manager.py,sha256=FNQ9T-djbJM2SzRx99khybCjEF5vG-8pS6jEBHqo7og,1157
-waveorder/plugin/main_widget.py,sha256=jrI7c-jZ-rhxO3ACwG_Rl7Eb6Ttw0aMNbrspCH0s120,78011
-waveorder/plugin/tab_recon.py,sha256=SGI_xUCDauChyq9PfHXbGPvBtMqfgIeqfmMIkXCPK4M,128329
+waveorder/plugin/main_widget.py,sha256=Vf5Eve9ik_86mdsSbezacME96eFnDf7A9myDaCnHHt4,58098
+waveorder/plugin/tab_recon.py,sha256=kiMhTa6sxqmQAYw9gGpcu66y0vEB-_e5mMAP7V136qU,131698
 waveorder/scripts/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 waveorder/scripts/launch_napari.py,sha256=0Sx_2XCJ38pBfe7QvthUn0Vu8ZcqD6qHjwBvzR6V2JY,221
 waveorder/scripts/repeat-cal-acq-rec.py,sha256=XVdQSoTacNczd58MBty4Qa4umprdUkgiwCkWQQr7p4g,3908
@@ -62,9 +61,9 @@ waveorder/visuals/jupyter_visuals.py,sha256=6kxICjEtP1qc1EuETc_NJ6Y4A7nVaC-bP3wl
 waveorder/visuals/matplotlib_visuals.py,sha256=v1zi0ZlXEV5CcpNzTWL0vDJ2Md2-RSHnc3rAB61wimg,10915
 waveorder/visuals/napari_visuals.py,sha256=bDEgHvoexdsGW4pIbnLfBCU4e4be41PMyKx9Mq9so1c,2361
 waveorder/visuals/utils.py,sha256=QC5WSc2yzPMjk66IjA39iNFgO_0It6evma201hH8Lg4,1001
-waveorder-3.0.0a2.dist-info/licenses/LICENSE,sha256=v_wJE3YLyTOjHj0kgPB9hP9YDieI0WMw7XjOgTmIr2c,1509
-waveorder-3.0.0a2.dist-info/METADATA,sha256=BlCdzh-GSlirBjMdYRegfgRRa8iIZQ_Da81IxxYHgME,14783
-waveorder-3.0.0a2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-waveorder-3.0.0a2.dist-info/entry_points.txt,sha256=cOCI4v8cdinVJiyAMlYZtxK6GCS4GF6Qpk1hTsgW18Y,106
-waveorder-3.0.0a2.dist-info/top_level.txt,sha256=i3zReXiiMTnyPk93W7aEz_oEfsLnfR_Kzl7PW7kUslA,10
-waveorder-3.0.0a2.dist-info/RECORD,,
+waveorder-3.0.0a3.dist-info/licenses/LICENSE,sha256=MATRcU1PWMarfKd4-d4q6eMdy4JWzC6fpavJI_zXHeE,2068
+waveorder-3.0.0a3.dist-info/METADATA,sha256=TLwY7IBS3b8wdV9CBwA0lYARs3KOyHlxmVAA7z6m6fQ,15576
+waveorder-3.0.0a3.dist-info/WHEEL,sha256=wUyA8OaulRlbfwMtmQsvNngGrxQHAvkKcvRmdizlJi0,92
+waveorder-3.0.0a3.dist-info/entry_points.txt,sha256=cOCI4v8cdinVJiyAMlYZtxK6GCS4GF6Qpk1hTsgW18Y,106
+waveorder-3.0.0a3.dist-info/top_level.txt,sha256=i3zReXiiMTnyPk93W7aEz_oEfsLnfR_Kzl7PW7kUslA,10
+waveorder-3.0.0a3.dist-info/RECORD,,

{waveorder-3.0.0a2.dist-info → waveorder-3.0.0a3.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.9.0)
+Generator: setuptools (80.10.2)
 Root-Is-Purelib: true
 Tag: py3-none-any
 

{waveorder-3.0.0a2.dist-info → waveorder-3.0.0a3.dist-info}/licenses/LICENSE

@@ -26,3 +26,15 @@ SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
 CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
 OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+## License Notice for Dependencies
+
+This repository is licensed under the BSD License; however, it relies on certain 
+third-party dependencies that are licensed under the GNU General Public License 
+(GPL). Specifically:
+
+- PyQt5 is licensed under the GNU General Public License v3 or later (GPLv3+).
+This library is not included in this repository but must be installed separately
+by users. Please be aware that the GPL license terms apply to these 
+dependencies, and certain uses of GPL-licensed code may have licensing 
+implications for your own software.