Merge branch 'test_image_reconstruct' into perf-streamdaq

miniscope_io/cli.py

@@ -0,0 +1,11 @@
+import click
+from miniscope_io.commands.capture import sdaqprof
+
+@click.group()
+def cli():
+    pass
+
+cli.add_command(sdaqprof)
+
+if __name__ == '__main__':
+    cli()

miniscope_io/commands/capture.py

@@ -0,0 +1,26 @@
+import click
+import os
+
+from pathlib import Path
+
+
+from miniscope_io.stream_daq import StreamDaqConfig, StreamDaq
+from miniscope_io.utils import hash_video, hash_file
+
+@click.command()
+@click.option('-c', '--config', required=True, help='YAML file to configure the streamDaq')
+@click.option('-s', '--source', required=False, help='RAW FPGA data to plug into okDevMock')
+@click.option('-o', '--output', default='output', help='Video output filename')
+def sdaqprof(config, source, output):
+
+    output_video = Path("output") / (output + ".avi")
+
+    if source:
+        # environment variable to allow import okDevMock
+        os.environ['STREAMDAQ_PROFILERUN'] = 'just_placeholder'
+        os.environ['PYTEST_OKDEV_DATA_FILE'] = source
+
+    daqConfig = StreamDaqConfig.from_yaml(config)
+
+    daq_inst = StreamDaq(config=daqConfig)
+    daq_inst.capture(source="fpga", video=output_video)

miniscope_io/stream_daq.py

@@ -230,7 +230,7 @@ def _uart_recv(
     def _init_okdev(self, BIT_FILE: Path) -> Union[okDev, okDevMock]:
 
         # FIXME: when multiprocessing bug resolved, remove this and just mock in tests
-        dev = okDevMock() if os.environ.get("PYTEST_CURRENT_TEST") is not None else okDev()
+        dev = okDevMock() if os.environ.get("PYTEST_CURRENT_TEST") or os.environ.get("STREAMDAQ_PROFILERUN") else okDev()
 
         dev.uploadBit(str(BIT_FILE))
         dev.setWire(0x00, 0b0010)

pyproject.toml

@@ -55,6 +55,7 @@ black = {version="^24.1.1", optional=true}
 ruff = {version="^0.2.0", optional=true}
 pre-commit = {version = "^3.7.1", optional = true}
 nox = {version = ">=2024.4.15", optional = true}
+click = "^8.1.7"
 
 [tool.poetry.extras]
 tests = ["pytest", "pytest-timeout", "matplotlib"]
@@ -73,6 +74,7 @@ requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
 
 [tool.poetry.scripts]
+mio = "miniscope_io.cli:cli"
 streamDaq = "miniscope_io.stream_daq:main"
 updateDevice = "miniscope_io.device_update:updateDevice"