remove pyqt6 dependency and re-worked setup cfgs

.github/ISSUE_TEMPLATE/bug_report.md

@@ -17,6 +17,8 @@ assignees: ''
 
 **Screenshots or steps for reproduction (using napari GUI)**
 
+**Include relevant logs which are created next to the output dir, name of the dataset, yaml file(s) if encountering reconstruction errors.**
+
 **Expected behavior**
 A clear and concise description of what you expected to happen.
 

.github/workflows/pytests.yml

@@ -24,7 +24,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install ".[acq,dev]"
+          pip install ".[all,dev]"
 
       #    - name: Lint with flake8
       #      run: |

README.md

@@ -48,10 +48,16 @@ conda activate recOrder
 ```
 
 Install `recOrder-napari` with acquisition dependencies
-(napari and pycro-manager):
+(napari with PyQt6 and pycro-manager):
 
 ```sh
-pip install recOrder-napari[acq]
+pip install recOrder-napari[all]
+```
+
+Install `recOrder-napari` without napari, QtBindings (PyQt/PySide) and pycro-manager dependencies:
+
+```sh
+pip install recOrder-napari
 ```
 
 Open `napari` with `recOrder-napari`:

docs/development-guide.md

@@ -19,7 +19,7 @@
 
     ```sh
     cd recOrder
-    pip install -e ".[acq,dev]"
+    pip install -e ".[all,dev]"
     ```
 
 4. Optionally, for the co-development of [`waveorder`](https://github.com/mehta-lab/waveorder) and `recOrder`:

docs/microscope-installation-guide.md

@@ -40,7 +40,7 @@ conda activate recOrder
 
 Install `recOrder` with acquisition dependencies (napari and pycro-manager):
 ```
-pip install recOrder-napari[acq]
+pip install recOrder-napari[all]
 ```
 Check your installation:
 ```

docs/napari-plugin-guide.md

@@ -160,6 +160,36 @@ Examples of acquiring 2D birefringence data (kidney tissue) with this snap metho
 
 See the [reconstruction guide](./reconstruction-guide.md) for CLI usage instructions. 
 
+## Reconstruction Tab
+The **Reconstruction** tab is designed to reconstruct `birefriengence, phase, birefrignence with phase, and flurescenece` datasets that have been either acquired or coverted to `.zarr` store as well as acquisitions that are in progress.
+
+![](./images/reconstruction_data.png)
+
+The **Input Store** and **Output Directory** point to the input and output `.zarr` data locations. Once an Input Store is selected some metadata parameters can be viewed by hovering the cursor over the `info label` ⓘ.
+
+![](./images/reconstruction_models.png)
+
+A `Model` defines the reconstruction parameters. Multiple models can be run against a dataset with varying parameters. The model generates a configuration file `.yml`, then uses the CLI to reconstruct the data with the configuration file, which makes all reconstructions exactly reproducible via a CLI.
+* **New**: Builds a model based on the `Checkbox` selection.
+* **Load**: Allows a model to be imported using a previous reconstruction `.yml` file.
+* **Clear**: This will clear all defined models.
+
+![](./images/reconstruction_birefriengence.png)
+
+Once a `New` model is built, it is pre-populated with default values that can be accessed by clicking on the ► icon and the parameters can be changed as required.
+See the [reconstruction guide](./reconstruction-guide.md) for further information on the parameters.
+
+![](./images/reconstruction_queue.png)
+
+Once the **RUN** button is triggered, the reconstruction will proceed based on the defined model(s) concurrently.
+
+> [!CAUTION]
+> Since the models run concurrently, it is the users responsibility to manage compute resources accordingly on a local or SLURM system.
+
+The `Reconstruction Queue` section will display the progress of the reconstruction in the form of text output. Once a reconstruction finishes the queue will self clear. Only in the case of any issues or error that are encountered the entry will remain.
+
+Once the reconstruction processing finishes, based on the option `Show after Reconstruction` the reconstructed images will show up in the napari viewer.
+
 ## Visualizations
 When an **Orientation*** layer appears at the top of the layers list, `recOrder` will automatically color it with an HSV color map that indicates the orientation. 
 

recOrder/acq/acq_functions.py

@@ -5,8 +5,9 @@
 
 import numpy as np
 from iohub import read_micromanager
-from pycromanager import Studio
-
+try:
+    from pycromanager import Studio
+except:pass
 
 def generate_acq_settings(
     mm,

recOrder/cli/gui_widget.py

@@ -1,7 +1,13 @@
 import sys
-from PyQt6.QtWidgets import QApplication, QWidget, QVBoxLayout, QStyle
 import click
-from recOrder.plugin import tab_recon
+
+try:
+    from recOrder.plugin import tab_recon
+except:pass
+
+try:
+    from qtpy.QtWidgets import QApplication, QWidget, QVBoxLayout, QStyle
+except:pass
 
 try:
     import qdarktheme
@@ -38,4 +44,4 @@ def __init__(self):
         layout.addWidget(recon_tab.recon_tab_mainScrollArea)
 
 if __name__ == "__main__":
-    gui()
+    gui()

recOrder/cli/main.py

@@ -3,7 +3,9 @@
 from recOrder.cli.apply_inverse_transfer_function import apply_inv_tf
 from recOrder.cli.compute_transfer_function import compute_tf
 from recOrder.cli.reconstruct import reconstruct
-from recOrder.cli.gui_widget import gui
+try:
+    from recOrder.cli.gui_widget import gui
+except:pass
 
 
 CONTEXT = {"help_option_names": ["-h", "--help"]}
@@ -23,7 +25,9 @@ def cli():
 cli.add_command(reconstruct)
 cli.add_command(compute_tf)
 cli.add_command(apply_inv_tf)
-cli.add_command(gui)
+try:
+    cli.add_command(gui)
+except:pass
 
 if __name__ == "__main__":
-    cli()
+    cli()

recOrder/plugin/__init__.py

@@ -1,11 +1,9 @@
 # qtpy defaults to PyQt5/PySide2 which can be present in upgraded environments
-import qtpy
+try:
+    import qtpy
 
-if qtpy.PYQT5:
-    raise RuntimeError(
-        "Please remove PyQt5 from your environment with `pip uninstall PyQt5`"
-    )
-elif qtpy.PYSIDE2:
-    raise RuntimeError(
-        "Please remove PySide2 from your environment with `pip uninstall PySide2`"
-    )
+    qtpy.API_NAME # check qtpy API name - one is required for GUI
+
+except RuntimeError as error:
+    if type(error).__name__ == "QtBindingsNotFoundError":
+        print("WARNING: QtBindings (PyQT or PySide) was not found for GUI")

recOrder/plugin/main_widget.py

@@ -15,25 +15,33 @@
 import numpy as np
 import yaml
 from dask import delayed
-from napari import Viewer
-from napari.components import LayerList
-from napari.qt.threading import create_worker
-from napari.utils.events import Event
-from napari.utils.notifications import show_info, show_warning
 from numpy.typing import NDArray
 from numpydoc.docscrape import NumpyDocString
 from packaging import version
-from pycromanager import Core, Studio, zmq_bridge
 from qtpy.QtCore import Qt, Signal, Slot
 from qtpy.QtGui import QColor, QPixmap
 from qtpy.QtWidgets import QFileDialog, QSizePolicy, QSlider, QWidget
 from superqt import QDoubleRangeSlider, QRangeSlider
 from waveorder.waveorder_reconstructor import waveorder_microscopy
 
-from recOrder.acq.acquisition_workers import (
-    BFAcquisitionWorker,
-    PolarizationAcquisitionWorker,
-)
+try:
+    from pycromanager import Core, Studio, zmq_bridge
+except:pass
+
+try:
+    from napari import Viewer
+    from napari.components import LayerList
+    from napari.qt.threading import create_worker
+    from napari.utils.events import Event
+    from napari.utils.notifications import show_info, show_warning
+except:pass
+
+try:
+    from recOrder.acq.acquisition_workers import (
+        BFAcquisitionWorker,
+        PolarizationAcquisitionWorker,
+    )
+except:pass
 from recOrder.calib import Calibration
 from recOrder.calib.Calibration import LC_DEVICE_NAME, QLIPP_Calibration
 from recOrder.calib.calibration_workers import (
@@ -825,14 +833,23 @@ def connect_to_mm(self):
             # Order is important: If the bridge is created before Core, Core will not work
             self.bridge = zmq_bridge._bridge._Bridge()
             logging.debug("Established ZMQ Bridge and found Core and Studio")
-        except:
+        except NameError:
+            print("Is pycromanager package installed?")
+        except Exception as ex:
+            print(
+                    "Could not establish pycromanager bridge.\n"
+                    "Is Micro-Manager open?\n"
+                    "Is Tools > Options > Run server on port 4827 checked?\n"
+                    f"Are you using nightly build {RECOMMENDED_MM}?\n"
+            )
+            template = "An exception of type {0} occurred. Arguments:\n{1!r}"
+            message = template.format(type(ex).__name__, ", ".join(ex.args))
+            print(message)
             raise EnvironmentError(
-                (
                     "Could not establish pycromanager bridge.\n"
                     "Is Micro-Manager open?\n"
                     "Is Tools > Options > Run server on port 4827 checked?\n"
                     f"Are you using nightly build {RECOMMENDED_MM}?"
-                )
             )
 
         # Warn the user if there is a Micro-Manager/ZMQ version mismatch

recOrder/plugin/tab_recon.py

@@ -3,10 +3,9 @@
 from pathlib import Path
 
 from qtpy import QtCore
-from qtpy.QtCore import Qt, QEvent, QThread
+from qtpy.QtCore import Qt, QEvent, QThread, Signal
 from qtpy.QtWidgets import *
 from magicgui.widgets import *
-from PyQt6.QtCore import pyqtSignal
 
 from iohub.ngff import open_ome_zarr
 
@@ -15,11 +14,13 @@
 from magicgui.type_map import get_widget_class
 import warnings
 
-from napari import Viewer
+try:
+    from napari import Viewer
+    from napari.utils import notifications
+except:pass
 
 from recOrder.io import utils
 from recOrder.cli import settings, jobs_mgmt
-from napari.utils import notifications
 
 import concurrent.futures
 
@@ -533,25 +534,31 @@ def validate_input_data(
                     print(exc.args)
 
                 try:
-                    for _, pos in dataset.positions():
-                        axes = pos.zgroup.attrs["multiscales"][0]["axes"]
-                        string_array_n = [str(x["name"]) for x in axes]
-                        string_array = [
-                            str(x)
-                            for x in pos.zgroup.attrs["multiscales"][0][
-                                "datasets"
-                            ][0]["coordinateTransformations"][0]["scale"]
-                        ]
-                        string_scale = []
-                        for i in range(len(string_array_n)):
-                            string_scale.append(
-                                "{n}={d}".format(
-                                    n=string_array_n[i], d=string_array[i]
+                    string_pos = []
+                    i = 0
+                    for pos_paths, pos in dataset.positions():
+                        string_pos.append(pos_paths)
+                        if i == 0:
+                            axes = pos.zgroup.attrs["multiscales"][0]["axes"]
+                            string_array_n = [str(x["name"]) for x in axes]
+                            string_array = [
+                                str(x)
+                                for x in pos.zgroup.attrs["multiscales"][0][
+                                    "datasets"
+                                ][0]["coordinateTransformations"][0]["scale"]
+                            ]
+                            string_scale = []
+                            for i in range(len(string_array_n)):
+                                string_scale.append(
+                                    "{n}={d}".format(
+                                        n=string_array_n[i], d=string_array[i]
+                                    )
                                 )
-                            )
-                        txt = "\n\nScale: " + ", ".join(string_scale)
-                        self.data_input_Label.tooltip += txt
-                        break
+                            txt = "\n\nScale: " + ", ".join(string_scale)
+                            self.data_input_Label.tooltip += txt
+                        i += 1
+                    txt = "\n\nFOV: " + ", ".join(string_pos)
+                    self.data_input_Label.tooltip += txt
                 except Exception as exc:
                     print(exc.args)
 
@@ -3363,7 +3370,7 @@ def table_update_and_cleaup_thread(
                                 # this is the only case where row deleting occurs
                                 # we cant delete the row directly from this thread
                                 # we will use the exp_id to identify and delete the row
-                                # using pyqtSignal
+                                # using Signal
                                 # break - based on status
                             elif JOB_TRIGGERED_EXC in jobTXT:
                                 params["status"] = STATUS_errored_job
@@ -3643,7 +3650,7 @@ class ShowDataWorkerThread(QThread):
     """Worker thread for sending signal for adding component when request comes
     from a different thread"""
 
-    show_data_signal = pyqtSignal(str)
+    show_data_signal = Signal(str)
 
     def __init__(self, path):
         super().__init__()
@@ -3657,7 +3664,7 @@ class AddOTFTableEntryWorkerThread(QThread):
     """Worker thread for sending signal for adding component when request comes
     from a different thread"""
 
-    add_tableOTFentry_signal = pyqtSignal(str, bool, bool)
+    add_tableOTFentry_signal = Signal(str, bool, bool)
 
     def __init__(self, OTF_dir_path, bool_msg, doCheck=False):
         super().__init__()
@@ -3675,7 +3682,7 @@ class AddTableEntryWorkerThread(QThread):
     """Worker thread for sending signal for adding component when request comes
     from a different thread"""
 
-    add_tableentry_signal = pyqtSignal(str, str, dict)
+    add_tableentry_signal = Signal(str, str, dict)
 
     def __init__(self, expID, desc, params):
         super().__init__()
@@ -3691,7 +3698,7 @@ class AddWidgetWorkerThread(QThread):
     """Worker thread for sending signal for adding component when request comes
     from a different thread"""
 
-    add_widget_signal = pyqtSignal(QVBoxLayout, str, str, str, str)
+    add_widget_signal = Signal(QVBoxLayout, str, str, str, str)
 
     def __init__(self, layout, expID, jID, desc, wellName):
         super().__init__()
@@ -3711,7 +3718,7 @@ class RowDeletionWorkerThread(QThread):
     """Searches for a row based on its ID and then
     emits a signal to QFormLayout on the main thread for deletion"""
 
-    removeRowSignal = pyqtSignal(int, str)
+    removeRowSignal = Signal(int, str)
 
     def __init__(self, formLayout):
         super().__init__()
@@ -3818,7 +3825,7 @@ def setText(self, text):
         self.label.setText(text)
 
 class MyWidget(QWidget):
-    resized = pyqtSignal()
+    resized = Signal()
 
     def __init__(self):
         super().__init__()