Squash final todos for SmartScan refactor
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6 changed files with 62 additions and 40 deletions
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@ -11,6 +11,7 @@ from typing import Optional
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import threading
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import os
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import time
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from datetime import datetime
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from subprocess import SubprocessError
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from fastapi import HTTPException
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@ -267,10 +268,10 @@ class SmartScanThing(lt.Thing):
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starting_position = self._stage.position
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overlap = self.overlap
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dx, dy = self._calc_displacement_from_test_image(overlap)
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stitch_resize = stitching.STITCHING_RESOLUTION[0] / self.save_resolution[0]
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correlation_resize = stitching.STITCHING_RESOLUTION[0] / self.save_resolution[0]
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self._scan_logger.debug(
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f"Resizing images when stitching by a factor of {stitch_resize}"
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f"Resizing images when correlating by a factor of {correlation_resize}"
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)
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self._scan_logger.info(
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@ -297,10 +298,10 @@ class SmartScanThing(lt.Thing):
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dy=dy,
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autofocus_dz=autofocus_dz,
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autofocus_on=bool(autofocus_dz),
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start_time=time.strftime("%H_%M_%S-%d_%m_%Y"),
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start_time=datetime.now(),
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skip_background=self.skip_background,
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stitch_automatically=self.stitch_automatically,
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stitch_resize=stitch_resize,
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correlation_resize=correlation_resize,
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save_resolution=self.save_resolution,
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)
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@ -338,7 +339,7 @@ class SmartScanThing(lt.Thing):
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self._preview_stitcher = stitching.PreviewStitcher(
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self._ongoing_scan.images_dir,
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overlap=self._scan_data.overlap,
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correlation_resize=self._scan_data.stitch_resize,
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correlation_resize=self._scan_data.correlation_resize,
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)
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# This is the main loop of the scan!
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@ -471,7 +472,7 @@ class SmartScanThing(lt.Thing):
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logger=self._scan_logger,
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cancel=self._cancel,
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scan_name=self._ongoing_scan.name,
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stitch_resize=self._scan_data.stitch_resize,
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correlation_resize=self._scan_data.correlation_resize,
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overlap=self._scan_data.overlap,
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)
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@ -691,7 +692,7 @@ class SmartScanThing(lt.Thing):
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logger: lt.deps.InvocationLogger,
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cancel: lt.deps.CancelHook,
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scan_name: str,
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stitch_resize: Optional[float] = None,
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correlation_resize: Optional[float] = None,
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overlap: Optional[float] = None,
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) -> None:
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"""Generate a stitched image based on stage position metadata.
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@ -706,7 +707,7 @@ class SmartScanThing(lt.Thing):
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self._scan_dir_manager.img_dir_for(scan_name),
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logger=logger,
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overlap=overlap,
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correlation_resize=stitch_resize,
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correlation_resize=correlation_resize,
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stitch_tiff=self.stitch_tiff,
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scan_data_dict=scan_data_dict,
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)
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