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adding coordinates test commands #312

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Merged
JoQCcoz merged 1 commit into from
Aug 9, 2024
Merged

adding coordinates test commands #312

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25 changes: 21 additions & 4 deletions Smartscope/core/test_commands.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
import os
import sys
from pathlib import Path
from typing import List, Tuple
from typing import List, Tuple, Literal
import torch
import logging
import time
Expand Down Expand Up @@ -145,12 +145,26 @@ def test_protocol_command(microscope_id,detector_id,command, instance=None, inst
instance = SquareModel.objects.get(pk=instance)
microscope = Microscope.objects.get(pk=microscope_id)
detector = Detector.objects.get(pk=detector_id)
scopeInterface = select_microscope_interface(microscope)
scopeInterface, additional_settings = select_microscope_interface(microscope)
with scopeInterface(microscope = micModels.Microscope.model_validate(microscope),
detector= micModels.Detector.model_validate(detector),
atlas_settings= micModels.AtlasSettings.model_validate(detector)) as scope:
atlas_settings= micModels.AtlasSettings.model_validate(detector),
additional_settings=additional_settings) as scope:
PROTOCOL_COMMANDS_FACTORY[command](scope,params,instance)

def run_microscope_command(microscope_id, detector_id, command, *args):
from Smartscope.core.models import Microscope, Detector
from Smartscope.core.interfaces.microscope_methods import select_microscope_interface
import Smartscope.core.interfaces.microscope as micModels
microscope = Microscope.objects.get(pk=microscope_id)
detector = Detector.objects.get(pk=detector_id)
scopeInterface, additional_settings = select_microscope_interface(microscope)
with scopeInterface(microscope = micModels.Microscope.model_validate(microscope),
detector= micModels.Detector.model_validate(detector),
atlas_settings= micModels.AtlasSettings.model_validate(detector),
additional_settings=additional_settings) as scope:
getattr(scope, command)(*args)


def list_plugins():
from Smartscope.core.settings.worker import PLUGINS_FACTORY
Expand Down Expand Up @@ -197,14 +211,17 @@ def test_find_hole_geometry(grid_id):
print(f'Updated grid {grid} with rotation: {rotation} degrees and spacing: {spacing} pixels.')


def test_image_to_stage_conversion(image_file, coords):
def test_image_to_stage_conversion(image_file, coords, coordinate_system:Literal['smartscope','serialem']='smartscope'):
from pathlib import Path
from Smartscope.lib.image.montage import Montage
from Smartscope.lib.image.target import Target

montage_file = Path(image_file)
montage = Montage(name=montage_file.stem)
montage.raw = montage_file
montage.load_or_process()
coords = [int(i) for i in coords.split(',')]
if coordinate_system == 'serialem':
coords = Target.flip_y(coords, montage.shape_y)
target = Target(coords, from_center=True)
target.convert_image_coords_to_stage(montage, compare=True)
9 changes: 5 additions & 4 deletions Smartscope/lib/image/target.py
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Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,8 @@ def set_area_radius(self, shape_type):
self.radius = min(len1, len2) / 2
# self.area = np.pi * (self.radius ** 2)

def flip_y(self, coords, shape_y):
@staticmethod
def flip_y(coords, shape_y):
flipped_coords= np.array([coords[0],shape_y - coords[1]])
logger.debug(f'Flipping y coords: {coords} to {flipped_coords}')
return flipped_coords
Expand All @@ -107,7 +108,7 @@ def convert_image_coords_to_stage(self, montage, force_legacy=False, compare=Fal
flipped_coords,
montage.metadata.iloc[tile].ImageToStageMatrix
)
logger.debug(f'\nUsed ImageToStageMatrix vectors {montage.metadata.iloc[tile].ImageToStageMatrix} to convert:\n\tY-flipped image coords: {flipped_coords} to\n\tStage coords: {self.stage_coords}')
logger.info(f'\nUsed ImageToStageMatrix vectors {montage.metadata.iloc[tile].ImageToStageMatrix} to convert:\n\tY-flipped image coords: {flipped_coords} to\n\tStage coords: {self.stage_coords}')
self.stage_z = montage.stage_z
if not compare:
return
Expand All @@ -119,10 +120,10 @@ def convert_image_coords_to_stage(self, montage, force_legacy=False, compare=Fal
montage.metadata.iloc[tile].TiltAngle,
return_vector=True
)
logger.debug(f'\nUsed mdoc-derived vector {vector.tolist()} to convert:\n\tImage coords: {self.coords} to\n\tStage coords: {self.stage_coords}')
logger.info(f'\nUsed mdoc-derived vector {vector.tolist()} to convert:\n\tImage coords: {self.coords} to\n\tStage coords: {self.stage_coords}')
self.stage_z = montage.stage_z
mdoc_to_stage = np.array([self.stage_x, self.stage_y])
if compare:
difference = is_to_stage - mdoc_to_stage
logger.debug(f'Difference between ImageToStageMatrix and mdoc-derived vectors: {difference} microns')
logger.info(f'Difference between ImageToStageMatrix and mdoc-derived vectors: {difference} microns')
return is_to_stage, mdoc_to_stage, difference