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stephen-riggsstephen-riggs
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Database will only allow simple types
1 parent 1167df7 commit 277eb8c

4 files changed

Lines changed: 163 additions & 76 deletions

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‎src/murfey/client/contexts/tomo_metadata.py‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -175,7 +175,9 @@ def post_transfer(
175175
"m22": float(key_val["a:Value"]["b:_m22"]),
176176
}
177177
if not stage_matrix or not image_matrix:
178-
print("No matrix found")
178+
logger.error(
179+
f"No stage or image shift matrix found for {transferred_file}"
180+
)
179181

180182
ref_matrix = {
181183
"m11": float(

‎src/murfey/util/db.py‎

Lines changed: 12 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -622,9 +622,18 @@ class SearchMap(SQLModel, table=True): # type: ignore
622622
pixel_size: Optional[float] = None
623623
image: str = ""
624624
binning: Optional[float] = None
625-
reference_matrix: Optional[dict[str, float]] = None
626-
stage_correction: Optional[dict[str, float]] = None
627-
image_shift_correction: Optional[dict[str, float]] = None
625+
reference_matrix_m11: Optional[float] = None
626+
reference_matrix_m12: Optional[float] = None
627+
reference_matrix_m21: Optional[float] = None
628+
reference_matrix_m22: Optional[float] = None
629+
stage_correction_m11: Optional[float] = None
630+
stage_correction_m12: Optional[float] = None
631+
stage_correction_m21: Optional[float] = None
632+
stage_correction_m22: Optional[float] = None
633+
image_shift_correction_m11: Optional[float] = None
634+
image_shift_correction_m12: Optional[float] = None
635+
image_shift_correction_m21: Optional[float] = None
636+
image_shift_correction_m22: Optional[float] = None
628637
width: Optional[int] = None
629638
height: Optional[int] = None
630639
session: Optional[Session] = Relationship(back_populates="search_maps")

‎src/murfey/util/models.py‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -145,9 +145,9 @@ class SearchMapParameters:
145145
pixel_size: Optional[float] = None
146146
image: Optional[str] = None
147147
binning: Optional[float] = None
148-
reference_matrix: Optional[dict[str, float]] = None
149-
stage_correction: Optional[dict[str, float]] = None
150-
image_shift_correction: Optional[dict[str, float]] = None
148+
reference_matrix: dict[str, float] = {}
149+
stage_correction: dict[str, float] = {}
150+
image_shift_correction: dict[str, float] = {}
151151
height: Optional[int] = None
152152
width: Optional[int] = None
153153
height_on_atlas: Optional[int] = None

‎src/murfey/util/tomo_metadata.py‎

Lines changed: 145 additions & 69 deletions
Original file line numberDiff line numberDiff line change
@@ -42,15 +42,53 @@ def register_search_map_in_database(
4242
search_map.pixel_size = search_map_params.pixel_size or search_map.pixel_size
4343
search_map.image = search_map_params.image or search_map.image
4444
search_map.binning = search_map_params.binning or search_map.binning
45-
search_map.reference_matrix = (
46-
search_map_params.reference_matrix or search_map.reference_matrix
45+
search_map.reference_matrix_m11 = (
46+
search_map_params.reference_matrix.get("m11")
47+
or search_map.reference_matrix_m11
4748
)
48-
search_map.stage_correction = (
49-
search_map_params.stage_correction or search_map.stage_correction
49+
search_map.reference_matrix_m12 = (
50+
search_map_params.reference_matrix.get("m12")
51+
or search_map.reference_matrix_m12
5052
)
51-
search_map.image_shift_correction = (
52-
search_map_params.image_shift_correction
53-
or search_map.image_shift_correction
53+
search_map.reference_matrix_m21 = (
54+
search_map_params.reference_matrix.get("m21")
55+
or search_map.reference_matrix_m21
56+
)
57+
search_map.reference_matrix_m22 = (
58+
search_map_params.reference_matrix.get("m22")
59+
or search_map.reference_matrix_m22
60+
)
61+
search_map.stage_correction_m11 = (
62+
search_map_params.stage_correction.get("m11")
63+
or search_map.stage_correction_m11
64+
)
65+
search_map.stage_correction_m12 = (
66+
search_map_params.stage_correction.get("m12")
67+
or search_map.stage_correction_m12
68+
)
69+
search_map.stage_correction_m21 = (
70+
search_map_params.stage_correction.get("m21")
71+
or search_map.stage_correction_m21
72+
)
73+
search_map.stage_correction_m22 = (
74+
search_map_params.stage_correction.get("m22")
75+
or search_map.stage_correction_m22
76+
)
77+
search_map.image_shift_correction_m11 = (
78+
search_map_params.image_shift_correction.get("m11")
79+
or search_map.image_shift_correction_m11
80+
)
81+
search_map.image_shift_correction_m12 = (
82+
search_map_params.image_shift_correction.get("m12")
83+
or search_map.image_shift_correction_m12
84+
)
85+
search_map.image_shift_correction_m21 = (
86+
search_map_params.image_shift_correction.get("m21")
87+
or search_map.image_shift_correction_m21
88+
)
89+
search_map.image_shift_correction_m22 = (
90+
search_map_params.image_shift_correction.get("m22")
91+
or search_map.image_shift_correction_m22
5492
)
5593
search_map.height = search_map_params.height or search_map.height
5694
search_map.width = search_map_params.width or search_map.width
@@ -78,9 +116,26 @@ def register_search_map_in_database(
78116
pixel_size=search_map_params.pixel_size,
79117
image=search_map_params.image,
80118
binning=search_map_params.binning,
81-
reference_matrix=search_map_params.reference_matrix,
82-
stage_correction=search_map_params.stage_correction,
83-
image_shift_correction=search_map_params.image_shift_correction,
119+
reference_matrix_m11=search_map_params.reference_matrix.get("m11"),
120+
reference_matrix_m12=search_map_params.reference_matrix.get("m12"),
121+
reference_matrix_m21=search_map_params.reference_matrix.get("m21"),
122+
reference_matrix_m22=search_map_params.reference_matrix.get("m22"),
123+
stage_correction_m11=search_map_params.stage_correction.get("m11"),
124+
stage_correction_m12=search_map_params.stage_correction.get("m12"),
125+
stage_correction_m21=search_map_params.stage_correction.get("m21"),
126+
stage_correction_m22=search_map_params.stage_correction.get("m22"),
127+
image_shift_correction_m11=search_map_params.image_shift_correction.get(
128+
"m11"
129+
),
130+
image_shift_correction_m12=search_map_params.image_shift_correction.get(
131+
"m12"
132+
),
133+
image_shift_correction_m21=search_map_params.image_shift_correction.get(
134+
"m21"
135+
),
136+
image_shift_correction_m22=search_map_params.image_shift_correction.get(
137+
"m22"
138+
),
84139
height=search_map_params.height,
85140
width=search_map_params.width,
86141
)
@@ -96,8 +151,8 @@ def register_search_map_in_database(
96151

97152
if all(
98153
[
99-
search_map.reference_matrix,
100-
search_map.stage_correction,
154+
search_map.reference_matrix_m11,
155+
search_map.stage_correction_m11,
101156
search_map.x_stage_position,
102157
search_map.y_stage_position,
103158
search_map.pixel_size,
@@ -110,25 +165,25 @@ def register_search_map_in_database(
110165
M = np.array(
111166
[
112167
[
113-
search_map.reference_matrix["m11"],
114-
search_map.reference_matrix["m12"],
168+
search_map.reference_matrix_m11,
169+
search_map.reference_matrix_m12,
115170
],
116171
[
117-
search_map.reference_matrix["m21"],
118-
search_map.reference_matrix["m22"],
172+
search_map.reference_matrix_m21,
173+
search_map.reference_matrix_m22,
119174
],
120175
]
121176
)
122177
B = np.array([search_map.x_stage_position, search_map.y_stage_position])
123178
R = np.array(
124179
[
125180
[
126-
search_map.stage_correction["m11"],
127-
search_map.stage_correction["m12"],
181+
search_map.stage_correction_m11,
182+
search_map.stage_correction_m12,
128183
],
129184
[
130-
search_map.stage_correction["m21"],
131-
search_map.stage_correction["m22"],
185+
search_map.stage_correction_m21,
186+
search_map.stage_correction_m22,
132187
],
133188
]
134189
)
@@ -152,6 +207,8 @@ def register_search_map_in_database(
152207
search_map.y_location = search_map_params.y_location
153208
if _transport_object:
154209
_transport_object.do_update_search_map(search_map.id, search_map_params)
210+
else:
211+
logger.info(f"Unable to register search map {search_map_name} position yet")
155212
murfey_db.add(search_map)
156213
murfey_db.commit()
157214
murfey_db.close()
@@ -188,61 +245,80 @@ def register_batch_position_in_database(
188245
)
189246

190247
# Get the pixel location on the searchmap
191-
M = np.array(
248+
if all(
192249
[
193-
[
194-
search_map.reference_matrix["m11"],
195-
search_map.reference_matrix["m12"],
196-
],
197-
[
198-
search_map.reference_matrix["m21"],
199-
search_map.reference_matrix["m22"],
200-
],
250+
search_map.reference_matrix_m11,
251+
search_map.stage_correction_m11,
252+
search_map.x_stage_position,
253+
search_map.y_stage_position,
254+
search_map.pixel_size,
255+
search_map.height,
256+
search_map.width,
201257
]
202-
)
203-
R1 = np.array(
204-
[
205-
[
206-
search_map.stage_correction["m11"],
207-
search_map.stage_correction["m12"],
208-
],
258+
):
259+
M = np.array(
209260
[
210-
search_map.stage_correction["m21"],
211-
search_map.stage_correction["m22"],
212-
],
213-
]
214-
)
215-
R2 = np.array(
216-
[
261+
[
262+
search_map.reference_matrix_m11,
263+
search_map.reference_matrix_m12,
264+
],
265+
[
266+
search_map.reference_matrix_m21,
267+
search_map.reference_matrix_m22,
268+
],
269+
]
270+
)
271+
R1 = np.array(
217272
[
218-
search_map.image_shift_correction["m11"],
219-
search_map.image_shift_correction["m12"],
220-
],
273+
[
274+
search_map.stage_correction_m11,
275+
search_map.stage_correction_m12,
276+
],
277+
[
278+
search_map.stage_correction_m21,
279+
search_map.stage_correction_m22,
280+
],
281+
]
282+
)
283+
R2 = np.array(
221284
[
222-
search_map.image_shift_correction["m21"],
223-
search_map.image_shift_correction["m22"],
224-
],
225-
]
226-
)
285+
[
286+
search_map.image_shift_correction_m11,
287+
search_map.image_shift_correction_m12,
288+
],
289+
[
290+
search_map.image_shift_correction_m21,
291+
search_map.image_shift_correction_m22,
292+
],
293+
]
294+
)
227295

228-
A = np.array([search_map.x_stage_position, search_map.y_stage_position])
229-
B = np.array([batch_parameters.x_stage_position, batch_parameters.y_stage_position])
296+
A = np.array([search_map.x_stage_position, search_map.y_stage_position])
297+
B = np.array(
298+
[batch_parameters.x_stage_position, batch_parameters.y_stage_position]
299+
)
230300

231-
vector_pixel = np.matmul(
232-
np.linalg.inv(M),
233-
np.matmul(np.linalg.inv(R1), np.matmul(np.linalg.inv(R2), np.matmul(M, B - A))),
234-
)
235-
centre_batch_pixel = vector_pixel / search_map.pixel_size + [
236-
search_map.width / 2,
237-
search_map.height / 2,
238-
]
239-
tilt_series.x_location = (
240-
centre_batch_pixel[0]
241-
- BatchPositionParameters.x_beamshift / search_map.pixel_size
242-
)
243-
tilt_series.y_location = (
244-
centre_batch_pixel[1]
245-
- BatchPositionParameters.y_beamshift / search_map.pixel_size
246-
)
301+
vector_pixel = np.matmul(
302+
np.linalg.inv(M),
303+
np.matmul(
304+
np.linalg.inv(R1), np.matmul(np.linalg.inv(R2), np.matmul(M, B - A))
305+
),
306+
)
307+
centre_batch_pixel = vector_pixel / search_map.pixel_size + [
308+
search_map.width / 2,
309+
search_map.height / 2,
310+
]
311+
tilt_series.x_location = (
312+
centre_batch_pixel[0]
313+
- BatchPositionParameters.x_beamshift / search_map.pixel_size
314+
)
315+
tilt_series.y_location = (
316+
centre_batch_pixel[1]
317+
- BatchPositionParameters.y_beamshift / search_map.pixel_size
318+
)
319+
else:
320+
logger.warning(
321+
f"No search map information available to register position of {batch_name}"
322+
)
247323
murfey_db.add(tilt_series)
248324
murfey_db.commit()

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