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Added calibration data download view

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This commit is contained in:
Joel Collins 2020-04-24 16:42:35 +01:00
parent cda5cdbb44
commit a1f3dd1624
1 changed files with 31 additions and 4 deletions
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35
openflexure_microscope/api/default_extensions/camera_stage_mapping/extension.py
View file

@ -6,26 +6,32 @@ This file contains the HTTP API for camera/stage calibration.
from labthings.server.view import View
from labthings.server.find import find_component
from labthings.server.extensions import BaseExtension
from labthings.server.decorators import marshal_task, ThingAction, use_args
from labthings.server.decorators import marshal_task, ThingAction, use_args, ThingProperty
from labthings.server import fields
from labthings.core.tasks import taskify
from labthings.core.utilities import get_by_path, set_by_path, create_from_path
from flask import abort, jsonify
from flask import abort, send_file
import logging
import time
import numpy as np
import PIL
import io
import os
import json
from .camera_stage_calibration_1d import calibrate_backlash_1d, image_to_stage_displacement_from_1d
from .camera_stage_tracker import Tracker
from openflexure_microscope.utilities import axes_to_array
from openflexure_microscope.paths import data_file_path
from openflexure_microscope.config import JSONEncoder
CSM_DATAFILE_NAME = "csm_calibration.json"
CSM_DATAFILE_PATH = data_file_path(CSM_DATAFILE_NAME)
class CSMExtension(BaseExtension):
"""
@ -39,6 +45,7 @@ class CSMExtension(BaseExtension):
)
_microscope = None
@property
def microscope(self):
# TODO: does caching the microscope actually help?
@ -96,12 +103,18 @@ class CSMExtension(BaseExtension):
# Combine X and Y calibrations to make a 2D calibration
cal_xy = image_to_stage_displacement_from_1d([cal_x, cal_y])
self.update_settings(cal_xy)
return {
data = {
"camera_stage_mapping_calibration": cal_xy,
"linear_calibration_x": cal_x,
"linear_calibration_y": cal_y,
}
with open(CSM_DATAFILE_PATH, 'w') as f:
json.dump(data, f, cls=JSONEncoder)
return data
@property
def image_to_stage_displacement_matrix(self):
try:
@ -161,7 +174,21 @@ class MoveInImageCoordinatesView(View):
"""Move the microscope stage, such that we move by a given number of pixels on the camera"""
csm_extension.move_in_image_coordinates(np.array([args.get("x"), args.get("y")]))
return jsonify(csm_extension.microscope.state["stage"]["position"])
return csm_extension.microscope.state["stage"]["position"]
csm_extension.add_view(MoveInImageCoordinatesView, "/move_in_image_coordinates")
@ThingProperty
class GetCalibrationFile(View):
def get(self):
"""Get the calibration data in JSON format."""
datafile_name = CSM_DATAFILE_NAME
datafile_path = CSM_DATAFILE_PATH
if os.path.isfile(datafile_path):
with open(datafile_path, 'rb') as f:
return json.load(f)
else:
return {}
csm_extension.add_view(GetCalibrationFile, "/get_calibration")