Gui testing take two (#119)

* first draft

* Added first version of GUI testing - browse tabs

* Added first version of GUI testing - browse tabs

* Fixing setup.py

* arrayqueues dep fix

* disabled GUI testing

* Testing only python 3.8

* fixed tests

* Not testing on windows because of vispy/OpenGL problems with pytest-qt

* Update main.yml

* Update main.yml

* Full exp test running now

* comments added

* removed unnecessary print, minor refactoring in streaming_save.py while debugging

Author: vigji

.github/workflows/main.yml

@@ -25,13 +25,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-latest, windows-latest]
-        python-version: [3.7, 3.8.6]
-        exclude:
-          - os: macos-latest
-            python-version: 3.7
-          - os: windows-latest
-            python-version: 3.7
+        os: [macos-latest]
+        python-version: [3.8.6]
     steps:
       - uses: actions/checkout@v2
       - name: Set up Python

.travis.yml

@@ -1,5 +1,5 @@
-arrayqueues==1.2.0b0
-flammkuchen==0.9
+arrayqueues==1.3.1
+split_dataset
 lightparam>=0.4, <0.5
 pyqt5>=5.15
 pyzmq

noxfile.py

@@ -0,0 +1,9 @@
+pytest-cov
+pytest-qt
+pytest
+gitpython
+coverage
+pre-commit
+black
+flake8
+isort

requirements.txt

@@ -56,12 +56,12 @@
     },
     "camera": {
         "id": 0,
-        "name": "hamamatsu",
+        "name": "mock",
         "max_sensor_resolution": [2048, 2048],
         "default_exposure": 60,
         "default_binning": 1,
     },
-    "light_source": {"name": "cobolt", "port": "COM4", "intensity_units": "mA"},
+    "light_source": {"name": "mock", "port": "COM4", "intensity_units": "mock"},
     "external_communication": {"name": "stytra", "address": "tcp://O1-589:5555"},
     "notifier": "none",
     "notifier_options": {},

requirements_dev.txt

@@ -511,7 +511,7 @@ def get_camera_properties(self):
                 "dcamprop_getname",
             )
 
-        if properties == {'': 0}:
+        if properties == {"": 0}:
             raise ConnectionError("The Hamamatsu camera seems to be off!")
 
         return properties

sashimi/config.py

@@ -12,6 +12,7 @@
 from sashimi.config import read_config
 from sashimi.processes.logging import LoggingProcess
 from sashimi.events import LoggedEvent, SashimiEvents
+from sashimi.utilities import get_last_parameters
 
 conf = read_config()
 
@@ -130,7 +131,8 @@ def fill_dataset(self, volume):
         if self.current_data is None:
             self.calculate_optimal_size(volume)
             self.current_data = np.empty(
-                (self.save_parameters.chunk_size, *volume.shape), dtype=self.dtype,
+                (self.save_parameters.chunk_size, *volume.shape),
+                dtype=self.dtype,
             )
 
         self.current_data[self.i_in_chunk, :, :, :] = volume
@@ -165,7 +167,10 @@ def finalize_dataset(self):
         ) as f:
             json.dump(
                 {
-                    "shape_full": (self.n_volumes, *self.current_data.shape[1:],),
+                    "shape_full": (
+                        self.n_volumes,
+                        *self.current_data.shape[1:],
+                    ),
                     "shape_block": (
                         self.save_parameters.chunk_size,
                         *self.current_data.shape[1:],
@@ -201,16 +206,17 @@ def calculate_optimal_size(self, volume):
         )
 
     def receive_save_parameters(self):
-        try:
-            self.save_parameters = self.saving_parameter_queue.get(timeout=0.001)
-        except Empty:
-            pass
-        try:
-            new_duration = self.duration_queue.get(timeout=0.001)
-            print(new_duration)
+        """Receive parameters on the stack shape from the `State` obj and new duration
+        from either the `EsternalTrigger` or the `State` if triggering is disabled.
+        """
+        # Get parameters:
+        parameters = get_last_parameters(self.saving_parameter_queue)
+        if parameters is not None:
+            self.save_parameters = parameters
+
+        # Get duration and update number of volumes:
+        new_duration = get_last_parameters(self.duration_queue)
+        if new_duration is not None:
             self.n_volumes = int(
                 np.ceil(self.save_parameters.volumerate * new_duration)
             )
-            print(self.n_volumes)
-        except Empty:
-            pass

sashimi/hardware/cameras/hamamatsu/interface.py

@@ -62,7 +62,7 @@ class TriggerSettings(ParametrizedQt):
     def __init__(self):
         super().__init__(self)
         self.name = "trigger_settings"
-        self.experiment_duration = Param(2_000, (1, 10_000), unit="s")
+        self.experiment_duration = Param(5, (1, 50_000), unit="s")
         self.is_triggered = Param(True, [True, False], gui=False)
 
 
@@ -71,7 +71,8 @@ def __init__(self):
         super().__init__()
         self.name = "general/scanning_state"
         self.scanning_state = Param(
-            "Paused", ["Paused", "Calibration", "Planar", "Volume"],
+            "Paused",
+            ["Paused", "Calibration", "Planar", "Volume"],
         )
 
 
@@ -183,7 +184,11 @@ def __init__(self):
 
     def add_calibration_point(self):
         self.calibrations_points.append(
-            (self.z_settings.piezo, self.z_settings.lateral, self.z_settings.frontal,)
+            (
+                self.z_settings.piezo,
+                self.z_settings.lateral,
+                self.z_settings.frontal,
+            )
         )
         self.calculate_calibration()
 
@@ -219,7 +224,8 @@ def calculate_calibration(self):
 
 
 def get_voxel_size(
-    scanning_settings: ZRecordingSettings, camera_settings: CameraSettings,
+    scanning_settings: ZRecordingSettings,
+    camera_settings: CameraSettings,
 ):
     scan_length = (
         scanning_settings.piezo_scan_range[1] - scanning_settings.piezo_scan_range[0]
@@ -522,7 +528,9 @@ def send_scansave_settings(self):
 
         elif self.global_state == GlobalState.PLANAR_PREVIEW:
             params = convert_single_plane_params(
-                self.planar_setting, self.single_plane_settings, self.calibration,
+                self.planar_setting,
+                self.single_plane_settings,
+                self.calibration,
             )
 
         elif self.global_state == GlobalState.VOLUME_PREVIEW:
@@ -644,10 +652,13 @@ def get_waveform(self):
             return None
 
     def calculate_pulse_times(self):
-        return np.arange(
-            self.volume_setting.n_skip_start,
-            self.volume_setting.n_planes - self.volume_setting.n_skip_end,
-        ) / (self.volume_setting.frequency * self.volume_setting.n_planes)
+        return (
+            np.arange(
+                self.volume_setting.n_skip_start,
+                self.volume_setting.n_planes - self.volume_setting.n_skip_end,
+            )
+            / (self.volume_setting.frequency * self.volume_setting.n_planes)
+        )
 
     def set_trigger_mode(self, mode: bool):
         if mode:

sashimi/processes/streaming_save.py

@@ -4,23 +4,32 @@
 with open("requirements.txt") as f:
     requirements = f.read().splitlines()
 
+with open("requirements_dev.txt") as f:
+    requirements_dev = f.read().splitlines()
+
+with open("README.md") as f:
+    long_description = f.read()
+
 setup(
     name="sashimi",
     version="0.2.0",
     author="Vilim Stih @portugueslab",
     author_email="vilim@neuro.mpg.de",
     packages=find_packages(),
     install_requires=requirements,
-    python_requires=">=3.7",
+    extras_require=dict(dev=requirements_dev),
+    python_requires=">=3.8",
     classifiers=[
         "Development Status :: 2 - Pre-Alpha",
         "Intended Audience :: Science/Research",
         "Natural Language :: English",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
     ],
     keywords="imaging microscopy lightsheet",
     description="A user-friendly software for efficient control of digital scanned light sheet microscopes (DSLMs).",
+    long_description=long_description,
+    long_description_content_type="text/markdown",
+    url="https://github.com/portugueslab/sashimi",
     entry_points={
         "console_scripts": [
             "sashimi=sashimi.main:main",