Gui update (#458)

* update cli to take one position, update apply inv tranf one to position to cli and comment slurm

* fixes for GUI

fixes to make the GUI compatible with updated libs
reworked client/server socket setup for propagating CLI progress

* git merge

* Update utils.py

* Update compute_transfer_function.py

* Update apply_inverse_transfer_function.py

* fixes

- formatting, jobs_mgmt bug

* test run needs to wait

since CLI is running in a separate thread, assert for file check needs to wait. for now we are using 60s for the reconstruction to finish

* test case for client/server socket., formatting

- implemented client/server feedback strategy to test case
- formatting

* test_cli_apply_inv_tf_output fix

test_cli_apply_inv_tf_output seems to do an assert check on captured text. implemented an output from the client/server strategy

* test_cli_apply_inv_tf_output text out

* re-worked jobs management/implementation

- removed client/server sockets implementation
- process are now managed by subprocess for updating GUI
- removed extraneous code from CLI related to sockets implementation/jobs mgmt

* Update tab_recon.py

fix import / styling

* Update tab_recon.py

- expand first model by default

* Update tab_recon.py

- styling

* Update tab_recon.py

Updated comments, removed commented out code

* revert CLI to original, etc.

---------

Co-authored-by: Taylla Theodoro <[email protected]>

Author: amitabhverma

tests/cli_tests/test_reconstruct.py

@@ -140,6 +140,7 @@ def test_append_channel_reconstruction(tmp_input_path_zarr):
     utils.model_to_yaml(fluor_settings, fluor_config_path)
 
     # Apply birefringence reconstruction
+
     runner = CliRunner()
     runner.invoke(
         cli,
@@ -151,14 +152,17 @@ def test_append_channel_reconstruction(tmp_input_path_zarr):
             str(biref_config_path),
             "-o",
             str(output_path),
+            "-uid",
+            str("birefringence_reconstruction"),
         ],
         catch_exceptions=False,
     )
+
     assert output_path.exists()
     with open_ome_zarr(output_path) as dataset:
         assert dataset["0/0/0"]["0"].shape[1] == 4
 
-    # Append fluoresncence reconstruction
+    # Append fluorescence reconstruction
     runner.invoke(
         cli,
         [
@@ -169,10 +173,14 @@ def test_append_channel_reconstruction(tmp_input_path_zarr):
             str(fluor_config_path),
             "-o",
             str(output_path),
+            "-uid",
+            str("fluorescence_reconstruction"),
         ],
         catch_exceptions=False,
     )
+
     assert output_path.exists()
+
     with open_ome_zarr(output_path) as dataset:
         assert dataset["0/0/0"]["0"].shape[1] == 5
         assert dataset.channel_names[-1] == "GFP_Density3D"

waveorder/acq/acquisition_workers.py

@@ -598,7 +598,6 @@ def _reconstruct(self):
             transfer_function_dirpath=transfer_function_path,
             config_filepath=self.config_path,
             output_dirpath=reconstruction_path,
-            unique_id="waveorderAcq",
         )
 
         # Read reconstruction to pass to emitters

waveorder/cli/apply_inverse_transfer_function.py

@@ -9,13 +9,14 @@
 import torch.multiprocessing as mp
 from iohub import open_ome_zarr
 
-from waveorder.cli import apply_inverse_models, jobs_mgmt
+from waveorder.cli import apply_inverse_models
 from waveorder.cli.parsing import (
     config_filepath,
     input_position_dirpaths,
     output_dirpath,
     processes_option,
     transfer_function_dirpath,
+    unique_id,
 )
 from waveorder.cli.printing import echo_headline, echo_settings
 from waveorder.cli.settings import ReconstructionSettings
@@ -25,8 +26,6 @@
 )
 from waveorder.io import utils
 
-JM = jobs_mgmt.JobsManagement()
-
 
 def _check_background_consistency(
     background_shape, data_shape, input_channel_names
@@ -107,6 +106,7 @@ def apply_inverse_transfer_function_single_position(
     num_processes,
     output_channel_names: list[str],
 ) -> None:
+
     echo_headline("\nStarting reconstruction...")
 
     # Load datasets
@@ -277,6 +277,7 @@ def apply_inverse_transfer_function_single_position(
     output_dataset.zattrs["settings"] = settings.dict()
 
     echo_headline(f"Closing {output_position_dirpath}\n")
+
     output_dataset.close()
     transfer_function_dataset.close()
     input_dataset.close()

waveorder/cli/compute_transfer_function.py

@@ -63,7 +63,9 @@ def generate_and_save_birefringence_transfer_function(settings, dataset):
 
 
 def generate_and_save_phase_transfer_function(
-    settings: ReconstructionSettings, dataset: Position, zyx_shape: tuple
+    settings: ReconstructionSettings,
+    dataset: Position,
+    zyx_shape: tuple,
 ):
     """Generates and saves the phase transfer function to the dataset, based on the settings.
 
@@ -150,7 +152,9 @@ def generate_and_save_phase_transfer_function(
 
 
 def generate_and_save_fluorescence_transfer_function(
-    settings: ReconstructionSettings, dataset: Position, zyx_shape: tuple
+    settings: ReconstructionSettings,
+    dataset: Position,
+    zyx_shape: tuple,
 ):
     """Generates and saves the fluorescence transfer function to the dataset, based on the settings.
 
@@ -187,7 +191,9 @@ def generate_and_save_fluorescence_transfer_function(
 
 
 def compute_transfer_function_cli(
-    input_position_dirpath: Path, config_filepath: Path, output_dirpath: Path
+    input_position_dirpath: Path,
+    config_filepath: Path,
+    output_dirpath: Path,
 ) -> None:
     """CLI command to compute the transfer function given a configuration file path
     and a desired output path.

waveorder/cli/gui_widget.py

@@ -13,7 +13,7 @@
     pass
 
 try:
-    import qdarktheme
+    import qdarktheme  # pip install pyqtdarktheme==2.1.0 --ignore-requires-python
 except:
     pass
 
@@ -31,7 +31,8 @@ def gui():
     )  # Other options: "Fusion", "Windows", "macOS", "WindowsVista"
     try:
         qdarktheme.setup_theme("dark")
-    except:
+    except Exception as e:
+        print(e.args)
         pass
     window = MainWindow()
     window.setWindowTitle(PLUGIN_ICON + " " + PLUGIN_NAME + " " + PLUGIN_ICON)

waveorder/cli/jobs_mgmt.py

@@ -106,3 +106,17 @@ def decorator(f: Callable) -> Callable:
         )(f)
 
     return decorator
+
+
+def unique_id() -> Callable:
+    def decorator(f: Callable) -> Callable:
+        return click.option(
+            "--unique-id",
+            "-uid",
+            default="",
+            required=False,
+            type=str,
+            help="Unique ID.",
+        )(f)
+
+    return decorator

waveorder/cli/parsing.py

@@ -13,6 +13,7 @@
     input_position_dirpaths,
     output_dirpath,
     processes_option,
+    unique_id,
 )
 
 
@@ -21,11 +22,13 @@
 @config_filepath()
 @output_dirpath()
 @processes_option(default=1)
+@unique_id()
 def _reconstruct_cli(
     input_position_dirpaths,
     config_filepath,
     output_dirpath,
     num_processes,
+    unique_id,
 ):
     """
     Reconstruct a dataset using a configuration file. This is a