Calibration: use a Scan Manager entry (pymodaq 5.3)

docs/src/user_guide/calibration.rst

@@ -29,7 +29,9 @@ Calibration Procedure
 ---------------------
 1. **Open the Calibration Tool**: Click **Calibration** |equalizer| in the toolbar or navigate to **Shaping > Calibration > Calibration**.
 
-2. **Select the SLM**: Ensure the **Shaper** module is loaded in PyMoDAQ’s Dashboard.
+2. **Select the SLM and the camera**: Ensure an actuator named **Shaper** (the SLM) and a detector named **Camera**
+   (seeing the fringes) are loaded in PyMoDAQ’s Dashboard. The scan configuration (``BeamShapingCalibration``
+   scanner, ``Shaper`` and ``Camera`` selected) is a Scan Manager entry shipped with the package.
 
 3. **Run Calibration**: The tool performs a **double-slit experiment**:
 

src/pymodaq_plugins_beam_shaping/scanners/calibration.py

@@ -4,7 +4,6 @@
 
 @author: Sebastien Weber
 """
-from cProfile import label
 from typing import List, Tuple, Any, TYPE_CHECKING
 import re
 import numpy as np

src/pymodaq_plugins_beam_shaping/scripts/make_calibration_entry.py

@@ -0,0 +1,56 @@
+"""Generate the Scan Manager entry used by the SLM calibration (resources/holography_calibration.scan)
+
+The entry selects the detector named Camera, the actuator named Shaper and the BeamShapingCalibration scanner. Only the
+names matter: mock modules are loaded in a Dashboard to create the entry with the Scan Manager itself, so it stays
+valid whatever the real camera and SLM are. Run it again if the format of the entries changes with PyMoDAQ.
+"""
+import sys
+import time
+from pathlib import Path
+
+from pymodaq.control_modules.enums import DAQTypesEnum
+from pymodaq.utils.managers.modules import ModuleType
+from pymodaq.utils.managers.modules.loader import PluginInfo
+
+from pymodaq_plugins_beam_shaping.utilities.calibrating import CALIBRATION_ENTRY
+
+
+def create_dashboard_with_camera_and_shaper(qapp, timeout=20.):
+    """ Create a Dashboard with a detector named Camera and an actuator named Shaper (mock ones)"""
+    from pymodaq.dashboard import create_load_dashboard
+
+    _, dashboard = create_load_dashboard()
+    dashboard.module_creator.load_created_modules([
+        [PluginInfo(id=1, name='Shaper', class_name='MockShaper', type=ModuleType.Actuator, do_init=False)],
+        [PluginInfo(id=2, name='Camera', class_name='MockShaperCamera', type=ModuleType.Detector, do_init=False,
+                    daq_type=DAQTypesEnum.DAQ2D)]])
+    start = time.time()
+    while time.time() - start < timeout and len(dashboard.modules_manager.modules_all) < 2:
+        qapp.processEvents()
+    return dashboard
+
+
+def main(entry_path: Path = CALIBRATION_ENTRY):
+    from pymodaq_gui.qt_utils import mkQApp
+    from pymodaq.extensions import DAQScan
+    from pymodaq.utils.gui_utils.loader_utils import create_extension
+
+    qapp = mkQApp('CalibrationEntry')
+    dashboard = create_dashboard_with_camera_and_shaper(qapp)
+    _, daq_scan = create_extension(dashboard, DAQScan)
+
+    scan_manager = daq_scan.scan_manager
+    modules = scan_manager.modules_manager
+    for name, selected in (('detectors', ['Camera']), ('actuators', ['Shaper'])):
+        modules.settings[name] = dict(all_items=modules.settings[name]['all_items'], selected=selected)
+    scan_manager.scanner.settings.child('scan_type').setValue('Scan1D')
+    scan_manager.scanner.settings.child('scan_sub_type').setValue('BeamShapingCalibration')
+
+    entry_path.unlink(missing_ok=True)
+    scan_manager.save_entries(entry_path)
+    print(f'Entry saved in {entry_path}')
+
+
+if __name__ == '__main__':
+    main()
+    sys.exit(0)

src/pymodaq_plugins_beam_shaping/utilities/calibrating.py

@@ -32,9 +32,9 @@
 logger = set_logger(get_module_name(__file__))
 
 
-# TODO: the xml file resources/holography_calibration.xml was a scan configuration of the pymodaq < 5.3 scanner manager
-# (ScanManager.get_scanner_folder no longer exists). It has to be rewritten as an entry of the scan manager of 5.3
-# (folder given by ScanManager.get_entry_folder) before BeamShapingCalibration can be used again.
+# Scan Manager entry (pymodaq >= 5.3) selecting the detector named Camera, the actuator named Shaper and the
+# BeamShapingCalibration scanner. It is generated by scripts/make_calibration_entry.py
+CALIBRATION_ENTRY = Path(__file__).parents[1].joinpath('resources', 'holography_calibration.scan')
 
 
 def check_monotonic(phases: np.ndarray) -> bool:
@@ -160,7 +160,7 @@ def do_things_after_ui_setup(self):
         self.show_widgets(False)
 
     def show_widgets(self, show=True):
-        for widget in (self.ui.dock_command, self.ui.get_toolbar('scan_manager')):
+        for widget in (self.dock_command, self.get_toolbar('scan_manager')):
             widget.setVisible(show)
 
     def do_things_after_experiment_set(self, experiment_name: str):
@@ -175,11 +175,7 @@ def do_things_after_experiment_set(self, experiment_name: str):
 
         if hasattr(self, 'scan_manager'):  #could happen because base class calls do_things_after_experiment_set before
             # scan_manager is set
-            self.scan_manager.entry = 'holography_calibration'
-            self.scan_manager.execute_entry()
-
-            QtWidgets.QApplication.processEvents()
-
+            self.scan_manager.execute_entry(CALIBRATION_ENTRY)
             self.connect_start_stop_step()
 
     def connect_start_stop_step(self):
@@ -227,6 +223,7 @@ def connect_things(self):
         self.scan_done_signal.connect(self.save_calibration)
 
     def save_calibration(self):
+        dwa_calibration = None
         with DataLoader(self.h5saver) as loader:
             try:
                 dwa_calibration = loader.load_data_from_name_origin(
@@ -265,7 +262,8 @@ def save_calibration(self):
                         saver.add_data(where=saver.raw_group, data=dwa_calibration)
             except NameError:
                 pass
-        self.show_calibration(show=True, calibration_dwa=dwa_calibration)
+        if dwa_calibration is not None:
+            self.show_calibration(show=True, calibration_dwa=dwa_calibration)
 
     @classmethod
     def get_calibration_dwa(cls) -> DataWithAxes:

tests/test_calibration.py

@@ -0,0 +1,50 @@
+"""The SLM calibration is a DAQScan whose scan configuration comes from a Scan Manager entry"""
+import numpy as np
+import pytest
+
+from pymodaq_data import DataRaw, DataToExport
+
+
+def test_calibration_scanner_phase_from_fringes(qtbot):
+    from types import SimpleNamespace
+    from pymodaq.utils.scanner.scanner import Scanner
+    import pymodaq_plugins_beam_shaping.scanners.calibration  # registers the scanner  # noqa: F401
+
+    shaper = SimpleNamespace(title='Shaper', units='')
+    scanner = Scanner(actuators=[shaper], selected_actuators=[shaper])
+    scanner.settings.child('scan_type').setValue('Scan1D')
+    scanner.settings.child('scan_sub_type').setValue('BeamShapingCalibration')
+    calibration = scanner.scanner
+    assert calibration.n_steps == 256
+
+    data = calibration.data_actuator_at(100)  # grey level on the right half of the SLM
+    assert data.as_grey_levels
+    assert set(np.unique(data[0])) == {0, 100}
+
+    x = np.arange(1024)
+    phases = []
+    for grey in range(0, 256, 32):
+        fringes = 100 + 50 * np.cos(2 * np.pi * x / 16 + grey / 255 * 3 * np.pi)
+        dwa = DataRaw('Camera', data=[np.tile(fringes, (50, 1))])
+        phase = calibration.process_data(DataToExport('Camera', data=[dwa])).get_data_from_name('Phase')
+        phases.append(phase[0][0])
+    assert np.unwrap(np.array(phases) - phases[0])[-1] == pytest.approx(224 / 255 * 3 * np.pi, rel=1e-2)
+
+
+def test_calibration_extension_uses_scan_manager_entry(qtbot, tmp_path, monkeypatch):
+    monkeypatch.chdir(tmp_path)  # the DAQScan creates its h5 file with a relative path on Linux
+    from pymodaq_gui.qt_utils import mkQApp
+    from pymodaq.utils.gui_utils.loader_utils import create_extension
+    from pymodaq_plugins_beam_shaping.scripts.make_calibration_entry import create_dashboard_with_camera_and_shaper
+    from pymodaq_plugins_beam_shaping.utilities.calibrating import BeamShapingCalibration, CALIBRATION_ENTRY
+
+    assert CALIBRATION_ENTRY.is_file()
+    dashboard = create_dashboard_with_camera_and_shaper(mkQApp('tests'))
+    win, calibration = create_extension(dashboard, BeamShapingCalibration)
+    calibration.do_things_after_experiment_set('test')
+
+    assert calibration.scan_manager.settings is not None
+    assert calibration.scanner.settings['scan_type'] == 'Scan1D'
+    assert calibration.scanner.settings['scan_sub_type'] == 'BeamShapingCalibration'
+    assert calibration.modules_manager.selected_actuators_name == ['Shaper']
+    assert calibration.modules_manager.selected_detectors_name == ['Camera']