Merge branch 'main' into video_services

Author: Baharis

docs/programs.md

@@ -28,6 +28,8 @@ These tools help calibrate instamatic for some experiments.
 - [instamatic.calibrate_movie_delays](#instamaticcalibrate_movie_delays) (`instamatic.calibrate.calibrate_movie_delays:main_entry`)
 - [instamatic.flatfield](#instamaticflatfield) (`instamatic.processing.flatfield:main_entry`)
 - [instamatic.stretch_correction](#instamaticstretch_correction) (`instamatic.processing.stretch_correction:main_entry`)
+- [instamatic.calibrate_stage_rotation](#instamaticcalibrate_stage_rotation) (`instamatic.calibrate.calibrate_stage_lowmag:main_entry`)
+
 
 **Tools**
 
@@ -176,6 +178,32 @@ instamatic.calibrate_stage_lowmag [-h] [IMG [IMG ...]]
 `-h`, `--help`
 : Show this help message and exit  
 
+## instamatic.calibrate_stage_rotation
+
+Program to calibrate and plan the rotation pace (in seconds / angle) against speed settings available on the microscope.
+
+**Usage:**  
+```bash
+instamatic.calibrate_stage_rotation [-h] [-a ALPHAS] [-s SPEEDS] [-m MODE] [-o OUTDIR]
+```
+
+**Optional arguments:**  
+
+`-h`, `--help`
+: Show this help message and exit  
+
+`-a ALPHAS`, `--alphas ALPHAS`
+: Comma-delimited list of alpha spans to calibrate (default: "1,2,3,4,5,6,7,8,9,10").
+
+`-s SPEEDS`, `--speeds SPEEDS`
+: Comma-delimited list of speed settings to calibrate (default: "0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0" or "1,2,3,4,5,6,7,8,9,10,11,12", whichever is accepted by the microscope).
+
+`-m MODE`, `--mode MODE`
+: Calibration mode to be used: "auto" - auto-determine upper and lower speed limits based on TEM response (default); "limited" - restrict TEM goniometer speed limits between min and max of --speeds; or "listed" - restrict TEM goniometer speed settings exactly to --speeds provided.
+
+`-o OUTDIR`, `--outdir OUTDIR`
+: Path to the directory where calibration file should be output (default: "%appdata%/calib" on Windows or "$AppData/calib" on Unix).
+
 
 ## instamatic.calibrate_stage_mag1
 

pyproject.toml

@@ -104,6 +104,7 @@ publishing = [
 "instamatic.calibrate_movie_delays" = "instamatic.calibrate.calibrate_movie_delays:main_entry"
 "instamatic.flatfield" = "instamatic.processing.flatfield:main_entry"
 "instamatic.stretch_correction" = "instamatic.processing.stretch_correction:main_entry"
+"instamatic.calibrate_stage_rotation" = "instamatic.calibrate.calibrate_stage_rotation:main_entry"
 # tools
 "instamatic.browser" = "scripts.browser:main"
 "instamatic.viewer" = "scripts.viewer:main"

src/instamatic/calibrate/__init__.py

@@ -5,5 +5,6 @@
 from .calibrate_directbeam import CalibDirectBeam
 from .calibrate_movie_delays import CalibMovieDelays
 from .calibrate_stage_lowmag import CalibStage
+from .calibrate_stage_rotation import CalibStageRotation
 
 # from .calibrate_stage_mag1 import CalibStageMag1

src/instamatic/calibrate/calibrate_movie_delays.py

@@ -73,10 +73,12 @@ def from_file(
         calib_conditions = (exposure, header_keys, header_keys_common)
         calib = calib_map.get(calib_conditions, None)
         if calib is None:
+            header_keys_str = ','.join(header_keys)
+            header_keys_common_str = ','.join(header_keys_common)
             raise KeyError(
                 f'Calibration for conditions {calib_conditions} not found. '
                 f"Please run 'instamatic.calibrate_movie_delays -e {exposure:.6f} "
-                f"-a {header_keys} -c {header_keys_common}' first."
+                f'-a "{header_keys_str}" -c "{header_keys_common_str}" first.'
             )
         return calib
 
@@ -188,8 +190,8 @@ def from_file(cls, path: Optional[str] = None) -> Self:
         if path is None:
             path = Path(calibration_drc) / CALIB_MOVIE_DELAYS
         try:
-            with open(Path(path), 'r') as json_file:
-                return cls.from_list(yaml.safe_load(json_file))
+            with open(Path(path), 'r') as yaml_file:
+                return cls.from_list(yaml.safe_load(yaml_file))
         except OSError as e:
             prog = 'instamatic.calibrate_movie_delays'
             raise OSError(f'{e.strerror}: {path}. Please run {prog} first.')
@@ -200,6 +202,7 @@ def to_file(self, path: Optional[str] = None) -> None:
             path = Path(calibration_drc) / CALIB_MOVIE_DELAYS
         with open(Path(path), 'w') as json_file:
             yaml.safe_dump(self.to_list(), json_file)
+        log(f'{self} saved to {path}.')
 
 
 class MovieTimes: