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This commit is contained in:
denis defolie
2026-05-04 19:05:40 +02:00
parent 3ecf0a1b6b
commit c0c3c37963
13 changed files with 134 additions and 48 deletions
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test_tube_scanner/make_videos.sh
+29 -4
View File
@@ -11,12 +11,37 @@ default_diameter=16.0 # mm
declare -A arguments=(
# key count length width fps duration seed bg-color arena-color arena-border shadow-color body-color body-dark body-light head-color thresh-immobile thresh-mobile thigmotaxis photo-mode photo-strength photo-x photo-y photo-sine-freq photo-radius chemo-strength chemo-x chemo-y chemo-radius avoid-strength avoid-radius aggreg-strength aggreg-radius chem-repulsion chem-decay
["A1"]="3 0.40 0.30 5 60 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
["A2"]="1 0.42 0.32 5 60 96 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 fixed 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["A3"]="1 0.50 0.40 5 60 128 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 radial 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["A1"]="4 0.40 0.30 15 600 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
)
declare -A arguments_all=(
# key count length width fps duration seed bg-color arena-color arena-border shadow-color body-color body-dark body-light head-color thresh-immobile thresh-mobile thigmotaxis photo-mode photo-strength photo-x photo-y photo-sine-freq photo-radius chemo-strength chemo-x chemo-y chemo-radius avoid-strength avoid-radius aggreg-strength aggreg-radius chem-repulsion chem-decay
["A1"]="3 0.40 0.30 15 60 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
["A2"]="1 0.42 0.32 15 60 96 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 fixed 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["A3"]="1 0.50 0.40 15 60 128 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 radial 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["A4"]="3 0.60 0.35 15 60 192 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.5 0.95"
["A5"]="1 0.30 0.32 15 60 250 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["A6"]="2 0.55 0.38 15 60 32 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 1.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["B1"]="3 0.40 0.30 15 60 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
["B2"]="1 0.42 0.32 15 60 96 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 fixed 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["B3"]="1 0.50 0.40 15 60 128 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 radial 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["B4"]="3 0.60 0.35 15 60 192 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.5 0.95"
["B5"]="1 0.30 0.32 15 60 250 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["B6"]="2 0.55 0.38 15 60 32 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 1.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["C1"]="3 0.40 0.30 15 60 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
["C2"]="1 0.42 0.32 15 60 96 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 fixed 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["C3"]="1 0.50 0.40 15 60 128 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 radial 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["C4"]="3 0.60 0.35 15 60 192 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.5 0.95"
["C5"]="1 0.30 0.32 15 60 250 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["C6"]="2 0.55 0.38 15 60 32 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 1.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["D1"]="3 0.40 0.30 15 60 64 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.45 none 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 1.0 3.0 0.0 6.0 0.0 0.95"
["D2"]="1 0.42 0.32 15 60 96 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 fixed 0.50 0.50 0.50 0.10 0.30 0.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["D3"]="1 0.50 0.40 15 60 128 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 radial 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["D4"]="3 0.60 0.35 15 60 192 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.5 0.95"
["D5"]="1 0.30 0.32 15 60 250 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 0.5 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
["D6"]="2 0.55 0.38 15 60 32 #EBEBEB #FAFAFA #8C8C8C #C8C8C8 #A5A5A5 #373737 #D2D2D2 #828282 0.2 1.5 0.70 none 0.50 0.50 0.50 0.10 0.30 1.0 0.70 0.70 2.0 0.0 3.0 0.0 6.0 0.0 0.95"
)
for key in "${!arguments[@]}"; do
args="${arguments[$key]}"
test_tube_scanner/modules/capture_interface.py
+4 -4
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@@ -99,13 +99,13 @@ class VideoCaptureInterface(abc.ABC):
def on_test_well_change(self, **cfg):
if self.use_tracking and cfg:
logger.warning(f"tracking conf: {cfg}")
self._tracker = PlanarianTracker(**cfg)
logger.warning(f"New tracker conf: {cfg}")
def on_well_change(self, cfg):
"""
Appelé par le CNC lors du changement de puits.
Appelé par la CNC lors du changement de puits.
Réinitialise le fond appris et l'état inter-frame du tracker.
Construit les métriques aussi
"""
@@ -119,8 +119,8 @@ class VideoCaptureInterface(abc.ABC):
min_area_px = self._params.min_area_px,
max_area_ratio = self._params.max_area_ratio,
max_planarians = self._params.planarian_count,
merge_kernel_size = settings.TRACKER_MERGE_KERNEL_SIZE,
min_contour_dist_px = settings.TRACKER_MIN_CONTOUR_DIST_PX,
merge_kernel_size = self._params.merge_kernel_size,
min_contour_dist_px = self._params.min_contour_dist_px,
)
test_tube_scanner/modules/planarian_metrics.py
+24 -4
View File
@@ -34,7 +34,7 @@ Métriques résumé (summary) :
Created on 25 avr. 2026
@author: denis
"""
import asyncio
import csv
import io
import json
@@ -659,13 +659,30 @@ class ReductStoreClient:
url: str = "http://localhost:8383",
token: str = "",
bucket: str = "planarian_metrics",
quota_type=None,
quota_size=1000_000_000
):
self.url = url
self.token = token
self.bucket_name = bucket
self.quota_type = quota_type
self.quota_size = quota_size
self._client = None
self._bucket = None
self._bucket = asyncio.run(self.create_bucket())
async def create_bucket(self):
from reduct import Client, BucketSettings
self._client = Client(self.url, api_token=self.token)
settings = BucketSettings(
quota_type=self.quota_type,
quota_size=self.quota_size,
exist_ok=True,
)
return await self._client.create_bucket(self.bucket_name, settings, exist_ok=True)
'''
async def connect(self):
"""Initialise la connexion et crée le bucket si nécessaire."""
from reduct import Client, BucketSettings, QuotaType
@@ -677,13 +694,16 @@ class ReductStoreClient:
)
logger.info(f"ReductStore connecté : {self.url} / {self.bucket_name}")
'''
async def store_metric(
self,
record: dict,
experiment: str,
well: str,
entry_name: str = "metrics",
planarian: int = 0,
record_type: str = "frame",
record_type: str = "metrics",
ts_us: Optional[int] = None,
):
"""Stocke un enregistrement dans ReductStore."""
@@ -691,7 +711,7 @@ class ReductStoreClient:
await self.connect()
ts_us = ts_us or int(time.time() * 1_000_000)
await self._bucket.write(
entry_name = "metrics",
entry_name = entry_name,
data = json.dumps(record).encode("utf-8"),
timestamp = ts_us,
labels = {
test_tube_scanner/modules/reductstore.py
+1 -1
View File
@@ -27,8 +27,8 @@ class ReductStoreBase(ABC):
self.bucket: Bucket = asyncio.run(self.create_bucket())
logger.info(f"==== {url} token:{api_token}")
async def create_bucket(self):
settings = BucketSettings(
quota_type=self.quota_type,
quota_size=self.quota_size,
test_tube_scanner/planarian/admin.py
+1 -1
View File
@@ -30,7 +30,7 @@ class ExperimentConfigAdmin(admin.ModelAdmin):
"classes": ("collapse",),
}),
(_("Tracker"), {
"fields": ("tube_axis", "min_area_px", "max_area_ratio", "planarian_count"),
"fields": ("tube_axis", "min_area_px", "max_area_ratio", "planarian_count", "merge_kernel_size", "min_contour_dist_px"),
"classes": ("collapse",),
}),
(_("Thigmotactisme"), {
test_tube_scanner/planarian/models.py
+14
View File
@@ -75,6 +75,18 @@ class ExperimentConfig(models.Model):
verbose_name=_("Nombre de planaires"),
)
merge_kernel_size = models.PositiveIntegerField(
_("Taille du kernel"),
help_text=_("taille du kernel elliptique de fusion des fragments (px)"),
default=15
)
min_contour_dist_px = models.PositiveIntegerField(
_("Distance <contour>"),
help_text=_("Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px."),
default=40
)
# --- Thigmotactisme ---
thigmotaxis_wall_dist_mm = models.FloatField(
default=1.0,
@@ -133,6 +145,8 @@ class ExperimentConfig(models.Model):
"tube_axis": self.tube_axis,
"min_area_px": self.min_area_px,
"max_area_ratio": self.max_area_ratio,
"merge_kernel_size": self.merge_kernel_size,
"min_contour_dist_px": self.min_contour_dist_px,
"planarian_count": self.planarian_count,
"thigmotaxis_wall_dist_mm": self.thigmotaxis_wall_dist_mm,
"photo_mode": self.photo_mode,
test_tube_scanner/planarian/templates/planarian/experiment_form.html
+15
View File
@@ -189,6 +189,21 @@
{% endif %}
</div>
<div class="w3-col m4 s12 w3-margin-bottom">
<label class="w3-text-grey"><b>{{ form.min_contour_dist_px.label }}</b></label>
{{ form.min_contour_dist_px }}
{% if form.min_contour_dist_px.errors %}
<span class="w3-text-red w3-small">{{ form.min_contour_dist_px.errors|join:", " }}</span>
{% endif %}
</div>
<div class="w3-col m4 s12 w3-margin-bottom">
<label class="w3-text-grey"><b>{{ form.merge_kernel_size.label }}</b></label>
{{ form.merge_kernel_size }}
{% if form.merge_kernel_size.errors %}
<span class="w3-text-red w3-small">{{ form.merge_kernel_size.errors|join:", " }}</span>
{% endif %}
</div>
</div>
</div>
</div>
test_tube_scanner/scanner/admin.py
+1 -1
View File
@@ -33,7 +33,7 @@ class ConfigurationAdmin(admin.ModelAdmin):
"fields": ("calibration_crop_radius", "calibration_default_multiwell", "calibration_default_feed", "calibration_default_step", "calibration_default_duration"),
"classes": ("collapse",),
}),
(_("Tracking"), {
(_("Tracking: valeurs par défaut"), {
"fields": ("tracking", "min_area_px", "max_area_ratio", "max_planarians", "merge_kernel_size", "min_contour_dist_px"),
"classes": ("collapse",),
}),
test_tube_scanner/scanner/models.py
-2
View File
@@ -66,13 +66,11 @@ class Configuration(models.Model):
calibration_default_duration = models.FloatField(_("Duruée calibration"), help_text=_("Durée de pose entre chaque puits en s"), default=3.0)
# tracking
tracking = models.BooleanField(_("Suivi"), help_text=_("Suivi et analyse des planaires"), default=False)
min_area_px = models.PositiveIntegerField(_("Surface minimale"), help_text=_("surface minimale d'un contour pour être considéré valide (px²)"), default=20)
max_area_ratio = models.FloatField(_("surface maximale "), help_text=_("surface maximale d'un contour en fraction de la frame (défaut 10%)"), default=0.10)
max_planarians = models.PositiveIntegerField(_("Max planaire"), help_text=_("nombre maximum de planaires à suivre simultanément (1-10)"), default=1)
merge_kernel_size = models.PositiveIntegerField(_("Taille du kernel"), help_text=_("taille du kernel elliptique de fusion des fragments (px)"), default=15)
min_contour_dist_px = models.PositiveIntegerField(_("Distance <contour>"), help_text=_("Distance min entre deux contours pour les considérer comme individus distincts. Défaut : 40px."), default=40)
#
active = models.BooleanField(_("Actif"), default=False)
test_tube_scanner/scanner/multiwell.py
+1 -1
View File
@@ -135,7 +135,7 @@ class MultiWellManager:
def _grid_scanning_capture(self, experiment, well_position, simulate=False):
well = well_position.well
multiwell = experiment.multiwell
if self.process.use_tracking:
# Paramètres d'une expérience PlanarianScanner
cfg = ExperimentConfig.objects.get(experiment_id=experiment.id, well_id=well.id)
# reset PlanarianTracker => on_well_change
test_tube_scanner/scanner/process.py
+33 -18
View File
@@ -21,7 +21,7 @@ from celery.exceptions import Ignore
from celery.utils.log import get_task_logger
from redis import Redis
from dataclasses import dataclass
from modules import reductstore, grbl, utils
from modules import reductstore, grbl, utils, planarian_metrics
## camera devices
from modules.circular_crop import CircularCrop, CropStrategy
@@ -42,6 +42,7 @@ class ProcessData:
logger = get_task_logger(__name__)
redisDB = Redis(host=settings.REDIS_HOST, port=settings.REDIS_PORT, db=0, decode_responses=True)
cameraDB = reductstore.ReductStore(name='camera')
planarianDB = planarian_metrics.ReductStoreClient(url=settings.REDUCTSTORE_URL, token=settings.REDUCTSTORE_TOKEN)
class CameraRecordManager():
@@ -183,14 +184,16 @@ class ScannerProcess(Task):
capture_type = self.conf.capture_type
if capture_type == 'file':
video_lists = []
wells = models.Well.objects.all()
for wl in wells:
if exists := (settings.MEDIA_ROOT / 'simulation' / f'{wl.name}.mp4').exists():
video_lists.append(str( settings.MEDIA_ROOT / 'simulation' / f'{wl.name}.mp4') )
from modules.videofile_capture import VideoFileCapture
self.cam = VideoFileCapture(
video_file=settings.MEDIA_ROOT / 'simulation' / 'D6.mp4',
video_file=settings.MEDIA_ROOT / 'simulation' / 'A1.mp4',
fps=self.video_fps,
width=self.video_width,
height=self.video_height,
@@ -272,13 +275,38 @@ class ScannerProcess(Task):
if self.grbl:
self._send(**msg)
def _store_metrics(self, uuid, metrics, ts):
for r in metrics:
pid = r["planarian_id"]
record = self.cam._metrics[pid].update(r, well_radius_mm=self.cam._params.well_radius_mm)
logger.warning(f"{record}")
async_to_sync(planarianDB.store_metrics)(
record,
self.cam._params.experiment,
self.cam._params.well_name,
entry_name=uuid,
planarian=pid,
record_type='metrics',
ts_us=ts,
)
def _store_frame(self, uuid, frame, ts, frame_count):
labels = {
"fps": self.video_fps,
"record_type": 'frame',
"frame_count": frame_count,
}
self.recordDB.write(uuid, frame, ts=ts, labels=labels)
def _on_frame(self, jpeg_bytes: bytes, ts: datetime, metrics: dict, frame_count: int = 0) -> None:
if self.data.record:
self.record_queue.put((self.data.uuid, ts, jpeg_bytes, metrics, frame_count))
if self.data.play:
try:
jpeg=base64.b64encode(jpeg_bytes).decode()
#logger.warning(f"{jpeg[:100]}")
self._send(ts=ts.timestamp(), jpeg=jpeg, frame_count=frame_count)
except Exception as e:
logger.error(f"----_on_frame: {e}")
@@ -289,21 +317,8 @@ class ScannerProcess(Task):
while not self.stop_event.is_set():
try:
(uuid, ts, frame, metrics, frame_count) = self.record_queue.get()
labels = dict(fps=self.video_fps, session=self.data.session, detected="1" if metrics.get("detected") else "0")
if metrics.get("detected"):
labels.update({
"cx" : str(metrics["cx"]),
"cy" : str(metrics["cy"]),
"area_px" : str(metrics["area_px"]),
"speed_px_s" : str(metrics["speed_px_s"]),
"axial_pos" : str(metrics["axial_pos"]),
"axial_speed" : str(metrics["axial_speed"]),
})
self.recordDB.write(uuid, frame, labels, ts=ts)
self._store_metrics(uuid, metrics, ts)
self._frame_store(uuid, frame, ts, frame_count)
self.record_queue.task_done()
except Exception as e:
logger.error(f'recorder: {e}')
test_tube_scanner/scanner/static/scanner/js/calibration.js
-1
View File
@@ -49,7 +49,6 @@ class ScannerManager {
this.merge_kernel_size = options.merge_kernel_size;
this.min_contour_dist_px = options.min_contour_dist_px;
this.track = options.track;
}
init_controls() {
test_tube_scanner/scanner/templates/scanner/calibration.html
+2 -2
View File
@@ -150,7 +150,7 @@
</div>
{% if conf.tracking %}
<div class="w3-row w3-row-padding w3-light-grey w3-margin-1 w3-round w3-round-large">
<div class="w3-col"><input id="_track" type="checkbox" value="0" onclick="if (this.checked){this.value='1';}else{ this.value='0';}">
<div class="w3-col"><input id="_track_it" type="checkbox" value="0" onclick="if (this.checked){this.value='1';}else{ this.value='0';}">
{% trans 'Configuration du tracking' %}
</div>
<div class="w3-half">
@@ -260,7 +260,7 @@
max_planarians : sId("_max_planarians"),
merge_kernel_size : sId("_merge_kernel_size"),
min_contour_dist_px : sId("_min_contour_dist_px"),
track : sId("_track")
track : sId("_track_it")
};
</script>
<script src="/static/scanner/js/calibration.js"></script>