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DAQ: added ml_bounding_box to loop centering, creates grid scan grid using ml. Fixed bug where filename wouldn't iterate for copied grid scans.

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This commit is contained in:
leonarski_f
2025-07-04 10:59:42 +02:00
parent 804d18db4d
commit 731efccc2b
8 changed files with 124 additions and 18 deletions
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common/src/aaredaqlib/models.py
+7
View File
@@ -94,6 +94,12 @@ class BeamMarkCoeffModel(BaseModel):
y=self.coeff_y[0] * zoom**2 + self.coeff_y[1] * zoom + self.coeff_y[2],
)
class BoundingBoxModel(BaseModel):
top_x: float
top_y: float
bottom_x: float
bottom_y: float
class LoopCenteringZoomModelElem(BaseModel):
zoom_value: float
@@ -177,6 +183,7 @@ class DAQStatusModel(BaseModel):
busy: bool
sample: SampleShortInfo | None = None
session: SessionStatus
box: BoundingBoxModel | None = None
class BeamlineSettingsModel(BaseModel):
dtz_max: float | None = 1600.0
daq/src/aaredaq/daq.py
+34 -10
View File
@@ -21,7 +21,7 @@ from aaredaqlib.models import (
SampleShortInfo,
PuckLoadedInfo,
SampleShortInfoList,
DAQStatusModel, BeamlineStatus, SessionStatus, SampleCameraSettings, AutofocusSettings, )
DAQStatusModel, BeamlineStatus, SessionStatus, SampleCameraSettings, AutofocusSettings, BoundingBoxModel, )
from aaredaqlib.raster_grid import RasterGridRequest, CompletedRasterGrid
from aaredaqlib.rotation_scan import RotationScanRequest, CompletedRotationScan
from aaredaqlib.sample_geometry import SampleGeometryModel
@@ -50,7 +50,8 @@ class AareDAQ:
self.__jfjoch = JFJochWrapper(bl)
self.__bl = bl.value.upper()
self.__aare = AareWrapper(bl)
self.__saved_box = None
@property
def state(self) -> BeamlineStateEnum:
return self.__cfg.state
@@ -80,6 +81,7 @@ class AareDAQ:
@omega.setter
def omega(self, val: float):
self.__cfg.set_busy(BeamlineStateEnum.SampleAlignment)
self.__saved_box = None
if -720 < val < 720:
self.__devs.aerotech.move(val, wait=True, speed=180.0, direct=True)
self.__cfg.state_busy = False
@@ -93,6 +95,7 @@ class AareDAQ:
@zoom.setter
def zoom(self, val: float):
self.__saved_box = None
self.__devs.zoom = val
@property
@@ -153,6 +156,7 @@ class AareDAQ:
new_meas_pos = self.__cfg.abr_meas_pos + c
self.__cfg.abr_meas_pos = new_meas_pos
self.__devs.abr_pos = new_meas_pos
self.__saved_box = None
self.__cfg.state_busy = False
except:
self.__cfg.state_busy = False
@@ -193,6 +197,7 @@ class AareDAQ:
def __mount(self, target: SampleShortInfo | None):
self.__set_state(BeamlineStateEnum.RobotSampleExchange)
self.__saved_box = None
self.__devs.smargon.move_home(wait=True)
self.__devs.abr_pos = ABR_POS_MOUNT
time.sleep(0.5)
@@ -433,6 +438,7 @@ class AareDAQ:
def smargon(self, sc: SmargonCoordinate):
self.__cfg.set_busy(BeamlineStateEnum.SampleAlignment)
try:
self.__saved_box = None
self.__devs.smargon.target = sc
self.__devs.smargon.wait()
self.__cfg.state_busy = False
@@ -495,7 +501,7 @@ class AareDAQ:
def listen_changes(self) -> redis.client.PubSub:
return self.__cfg.listen_changes()
def __ml_bounding_box(self, sample_id: int | None = None, filename: str | None = None, move: bool = False) -> None | Tuple[float, float, float, float]:
def __ml_bounding_box(self, sample_id: int | None = None, filename: str | None = None, move: bool = False) -> BoundingBoxModel | None:
time.sleep(0.2) # Just to be sure image is stable
#curr_image = self.camera_image
#box = self.__mlbox.predict(curr_image)
@@ -515,16 +521,33 @@ class AareDAQ:
coord = geom.picture_to_smargon(Coordinate(x=x1, y=y1))
self.__devs.smargon.target = SmargonCoordinate(sh_mm=coord)
self.__devs.smargon.wait(60)
return box
return BoundingBoxModel(bottom_x=x1, bottom_y=y1, top_x=x2, top_y=y2)
def ml_bounding_box(self, sample_id: int | None = None, filename: str | None = None, move: bool = False) -> None | Tuple[float, float, float, float]:
def ml_bounding_box(self, sample_id: int | None = None, filename: str | None = None, move: bool = False) -> RasterGridRequest | None:
try:
self.__cfg.try_set_busy(timeout=360)
box = self.__ml_bounding_box(sample_id, filename, move)
if not box:
raise LoopCenteringFailed
ml_box = self.__ml_bounding_box(sample_id, filename, move)
r = None
if ml_box is not None:
geom = self.sample_geometry
start_coord = geom.picture_to_smargon(Coordinate(x=ml_box.bottom_x, y=ml_box.bottom_y))
grid_size = Coordinate(x=geom.beam_size_mm.x * 0.8, y=geom.beam_size_mm.y * 0.8)
n_x = abs(ceil((ml_box.top_x - ml_box.bottom_x) * geom.pixel_in_mm / grid_size.x))
n_y = abs(ceil((ml_box.top_y - ml_box.bottom_y) * geom.pixel_in_mm / grid_size.y))
r = RasterGridRequest(
exp_time_s=0.05,
smargon= SmargonCoordinate(chi_deg = geom.smargon.chi_deg,
phi_deg= geom.smargon.phi_deg,
sh_mm=start_coord),
n_x=n_x,
n_y=n_y,
grid_size_mm= grid_size,
omega_deg=geom.omega_deg
)
self.__cfg.state_busy = False
return box
return r
except Exception:
self.__cfg.state_busy = False
raise
@@ -836,7 +859,8 @@ class AareDAQ:
bl=self.beamline_status,
sample=self.sample,
session=SessionStatus(),
diffraction=self.diffraction_geometry
diffraction=self.diffraction_geometry,
box=self.__saved_box
)
def cancel(self):
daq/src/aaredaq/server.py
+13 -5
View File
@@ -7,7 +7,8 @@ import urllib3
import uvicorn
from aaredaqlib.coordinate import SmargonCoordinate, Coordinate
from aaredaqlib.models import SampleShortInfo, DAQStatusModel, BeamlineStateEnum, BeamlineSettingsModel, \
SampleShortInfoList, SessionStatus, SampleCameraSettings, AutofocusSettings, TokenData
SampleShortInfoList, SessionStatus, SampleCameraSettings, AutofocusSettings, TokenData, \
CryojetSettingsModel
from aaredaqlib.raster_grid import RasterGridRequest, CompletedRasterGrid
from aaredaqlib.rotation_scan import RotationScanRequest, CompletedRotationScan
from aaredaqlib.sample_geometry import SampleGeometryModel
@@ -330,11 +331,9 @@ async def alc_center_loop(token: str = Depends(oauth2_scheme)) -> str:
@app.post("/alc/ml_bounding_box")
async def alc_ml_bounding_box(token: str = Depends(oauth2_scheme), move: bool = False, filename: str = "") -> Tuple[
float, float, float, float] | None:
async def alc_ml_bounding_box(token: str = Depends(oauth2_scheme)) -> RasterGridRequest | None:
auth.check_jwt_rw(cfg, auth.parse_token(token))
return daq.ml_bounding_box(move=move)
return daq.ml_bounding_box()
# Access management
@app.get("/access/pgroup")
@@ -387,6 +386,15 @@ async def put_settings(s: BeamlineSettingsModel, token: str = Depends(oauth2_sch
auth.check_jwt_staff(auth.parse_token(token))
cfg.settings = s
@app.get("/beamline/cryo_settings")
async def get_cryo_settings(token: str = Depends(oauth2_scheme)) -> CryojetSettingsModel:
auth.check_jwt_staff(auth.parse_token(token))
return cfg.cryojet_settings
@app.put("/beamline/cryo_settings")
async def put_cryo_settings(s: CryojetSettingsModel, token: str = Depends(oauth2_scheme)):
auth.check_jwt_staff(auth.parse_token(token))
cfg.cryojet_settings = s
LOGGING_CONFIG = {
"version": 1,
gui/src/aaregui/main_window.py
+3
View File
@@ -143,6 +143,9 @@ class MainWindow(QMainWindow):
self.beamline.samcam.changed.connect(self.daq.samcam_settings)
self.beamline.loopctr.background.clicked.connect(self.daq.alc_background)
self.beamline.loopctr.find_tip.clicked.connect(self.daq.center_loop)
self.beamline.loopctr.bounding_box.clicked.connect(self.daq.ml_bounding_box)
self.daq.raster_generated_by_ml.connect(self.raster.update_active_grid_request)
self.camera_image.smargon.connect(self.daq.move_smargon)
self.beamline.smargon_panel.smargon.connect(self.daq.move_smargon)
self.camera_image.samcam_updated.connect(self.daq.samcam_settings)
gui/src/aaregui/panels/loop_centering_panel.py
+5 -2
View File
@@ -8,11 +8,14 @@ class LoopCenteringPanel(QWidget):
super().__init__(parent)
grid_layout = QGridLayout(self)
grid_layout.addWidget(TitleLabel("Loop centering", self), 0, 0, 1, 2)
grid_layout.addWidget(TitleLabel("Loop centering", self), 0, 0, 1, 3)
grid_layout.setColumnStretch(0, 1)
grid_layout.setColumnStretch(1, 1)
self.find_tip = QPushButton("Center", parent=self)
grid_layout.addWidget(self.find_tip, 1, 0)
self.background = QPushButton("Background", parent=self)
self.background = QPushButton("Bkg", parent=self)
grid_layout.addWidget(self.background, 1, 1)
self.bounding_box = QPushButton("Box", parent=self)
grid_layout.addWidget(self.bounding_box, 1, 2)
gui/src/aaregui/scan_logic/raster_grid_manager.py
+19 -1
View File
@@ -123,6 +123,18 @@ class RasterGridManager(QObject):
return True
return False
@Slot(RasterGridRequest)
def update_active_grid_request(self, grid: RasterGridRequest):
self.__active_grid.smargon = grid.smargon
self.__active_grid.omega_deg = grid.omega_deg
self.__active_grid.grid_size_mm = grid.grid_size_mm
self.__active_grid.n_x = grid.n_x
self.__active_grid.n_y = grid.n_y
self.grid_scan_size_changed.emit(self.__active_grid.n_x,
self.__active_grid.n_y,
self.__active_grid.grid_size_mm.x,
self.__active_grid.grid_size_mm.y)
@Slot(DAQStatusModel)
def update_daq_status(self, s: DAQStatusModel):
if s.sample is not None and s.sample.db_id != self.__sample_id:
@@ -401,7 +413,13 @@ class RasterGridManager(QObject):
@Slot(int)
def completed_grid_redo(self, row: int):
if 0 <= row < len(self.__completed_grids):
self.__active_grid = copy.deepcopy(self.__completed_grids[row].request)
copy_of_active_grid = copy.deepcopy(self.__completed_grids[row].request)
self.__active_grid.n_x = copy_of_active_grid.n_x
self.__active_grid.n_y = copy_of_active_grid.n_y
self.__active_grid.grid_size_mm = copy_of_active_grid.grid_size_mm
self.__active_grid.smargon = copy_of_active_grid.smargon
self.__active_grid.omega_deg = copy_of_active_grid.omega_deg
self.__active_grid.visible = True
self.__completed_grids[row].request.visible = False
gui/src/aaregui/threads/daq_worker.py
+23
View File
@@ -23,6 +23,7 @@ class DAQWorker(QObject):
run_number_incremented = Signal()
raster_scan_completed = Signal(CompletedRasterGrid)
standard_scan_completed = Signal(CompletedRotationScan)
raster_generated_by_ml = Signal(RasterGridRequest)
def __init__(self, base_url: str | None, token: str, parent=None):
super().__init__(parent)
@@ -342,3 +343,25 @@ class DAQWorker(QObject):
@Slot()
def cancel(self):
self.generic_post("scan/cancel")
def handle_ml_box_response(self, reply):
try:
response_data = self.handle_response(reply)
if response_data != "":
parsed_response = RasterGridRequest.model_validate_json(response_data)
self.raster_generated_by_ml.emit(parsed_response)
except Exception as e:
print(e)
self.http_error.emit(str(e))
@Slot()
def ml_bounding_box(self):
if self.__base_url is None:
print(f"POST /alc/ml_bounding_box")
return
request = QNetworkRequest(QUrl(f"{self.__base_url}/alc/ml_bounding_box"))
request.setRawHeader(b"Authorization", f"Bearer {self.__token}".encode("utf-8"))
reply = self.__net_manager.post(request, QByteArray(b""))
reply.finished.connect(lambda: self.handle_ml_box_response(reply))
gui/src/aaregui/widgets/camera_image.py
+20
View File
@@ -72,6 +72,7 @@ class SampleCameraImageLabel(QGraphicsView):
self.__helical_start = SmargonCoordinate()
self.__helical_end = SmargonCoordinate()
self.__raster_alpha = 127
self.__bounding_box = None
self.start_point = None # Starting point of the rectangle
self.end_point = None # Ending point of the rectangle
@@ -106,6 +107,7 @@ class SampleCameraImageLabel(QGraphicsView):
self.right_click_hold_threshold = 200
def drawForeground(self, painter, rect):
self.__draw_ml_bounding_box(painter)
self.__draw_beam_center(painter)
self.__raster_mgr.draw_grid(painter, self.__raster_alpha)
self.__draw_helical(painter)
@@ -309,6 +311,8 @@ class SampleCameraImageLabel(QGraphicsView):
def update_daq_status(self, s: DAQStatusModel):
self.__geom = s.geom
self.__sam_cam = s.bl.sample_camera
self.__bounding_box = s.box
if s.state == BeamlineStateEnum.BeamLocation:
self.__state = SampleCameraImageState.BEAM_MARKING
elif self.__state == SampleCameraImageState.BEAM_MARKING:
@@ -332,6 +336,22 @@ class SampleCameraImageLabel(QGraphicsView):
)
self.smargon.emit(smargon_coord)
def __draw_ml_bounding_box(self, painter: QPainter):
if self.__bounding_box is None:
return
painter.setPen(QPen(QColor(50,205, 50), 3, Qt.PenStyle.SolidLine))
painter.setBrush(Qt.BrushStyle.NoBrush)
painter.drawRect(
QRect(
int(self.__bounding_box.bottom_x),
int(self.__bounding_box.bottom_y),
int(self.__bounding_box.top_x - self.__bounding_box.bottom_x),
int(self.__bounding_box.top_y - self.__bounding_box.bottom_y),
)
)
def __draw_beam_center(self, painter: QPainter):
beam_size_pxl = self.__geom.beam_size_pxl