denis/PlanarianScanner
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

simulation

Browse Source
This commit is contained in:
denis defolie
2026-05-03 23:11:00 +02:00
parent ce32bee3e8
commit ebdeb5f651
6 changed files with 1409 additions and 3 deletions
Download Patch File Download Diff File Expand all files Collapse all files
test_tube_scanner/home/settings.py
+1
View File
@@ -407,3 +407,4 @@ CALIBRATION_AUTO_DURATION = 45.0
CALIBRATION_AUTO_TIMEOUT = 2.5
test_tube_scanner/make_videos.sh
Executable
+56
View File
@@ -0,0 +1,56 @@
#!/bin/bash
# Génère 24 vidéos pour simuler le balayage d'un multi-puit de 6x24
# A1..A6, B1..B6, C1..C6, D1..D6
#
PATH="data"
default_width=1000 # px
default_height=1000 # px
default_diameter=16.0 # mm
declare -A arguments=(
# key count len width sec fps seed thigmotaxis bg-color arena-color arena-border shadow-color body-color body-dark body-light head-color
["F0"]="1 0.90 0.30 60 5 64 0.45 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5A7896 #3C5570 #8CA0B4 #46645F"
)
declare -A arguments2=(
# key count len width sec fps seed thigmotaxis bg-color arena-color arena-border shadow-color body-color body-dark body-light head-color
["D1"]="3 0.90 0.30 60 5 64 0.45 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5A7896 #3C5570 #8CA0B4 #46645F"
["D2"]="2 0.75 0.40 60 5 96 0.50 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5B7896 #3D5570 #8DA0B4 #47645F"
["D3"]="1 0.80 0.50 60 5 42 0.60 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["D4"]="1 0.85 0.40 60 5 28 0.70 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["D5"]="3 0.60 0.35 60 5 132 0.65 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["D6"]="2 0.65 0.35 60 5 256 0.85 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["C6"]="1 0.90 0.30 60 5 64 0.45 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5A7896 #3C5570 #8CA0B4 #46645F"
["C5"]="3 0.75 0.40 60 5 96 0.50 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5B7896 #3D5570 #8DA0B4 #47645F"
["C4"]="2 0.80 0.50 60 5 42 0.60 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["C3"]="1 0.85 0.40 60 5 28 0.70 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["C2"]="2 0.60 0.35 60 5 132 0.65 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["C1"]="3 0.65 0.35 60 5 256 0.85 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["B1"]="2 0.90 0.30 60 5 64 0.45 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5A7896 #3C5570 #8CA0B4 #46645F"
["B2"]="1 0.75 0.40 60 5 96 0.50 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5B7896 #3D5570 #8DA0B4 #47645F"
["B3"]="1 0.80 0.50 60 5 42 0.60 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["B4"]="3 0.85 0.40 60 5 28 0.70 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["B5"]="1 0.60 0.35 60 5 132 0.65 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["B6"]="2 0.65 0.35 60 5 256 0.85 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["A6"]="1 0.90 0.30 60 5 64 0.45 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5A7896 #3C5570 #8CA0B4 #46645F"
["A5"]="1 0.75 0.40 60 5 96 0.50 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5B7896 #3D5570 #8DA0B4 #47645F"
["A4"]="3 0.80 0.50 60 5 42 0.60 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["A3"]="1 0.85 0.40 60 5 28 0.70 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["A2"]="1 0.60 0.35 60 5 132 0.65 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
["A1"]="4 0.65 0.35 60 5 256 0.85 #D4DADC #BDBDF0 #B4AFA8 #BEBCB6 #5C7896 #3E5570 #8EA0B4 #48645F"
)
for key in "${!arguments[@]}"; do
args="${arguments[$key]}"
read -r count length width duration fps seed thigmotaxis bg_color arena_color arena_border shadow_color body_color body_dark body_light head_color <<< "$args"
echo "==== Exécution de $PATH/$key.mp4"
./planarian_sim.py --output "$PATH/$key.mp4" --default_width "$default_width" --default_height "$default_height" --default_diameter "$default_diameter" \
--count "$count" --length "$length" --width "$width" --duration "$duration" --fps "$fps" --seed "$seed" --thigmotaxis "$thigmotaxis" \
--bg-color "$bg_color" --arena-color "$arena_color" --arena-border "$arena_border" --shadow-color "$shadow_color" \
--body-color "$body_color" --body-dark "$body_dark" --body-light "$body_light" --head-color "$head_color" --no-csv
done
test_tube_scanner/planarian_sim.py
Executable
+1341
View File
File diff suppressed because it is too large Load Diff
test_tube_scanner/scanner/process.py
+4
View File
@@ -468,6 +468,10 @@ class ScannerProcess(Task):
msg = self.manager.set_well_position()
self._send(**msg)
elif topic == 'track':
self.cam.use_tracking = value=="1"
self._send(state=topic, msg=f"Tracking: {self.cam.use_tracking}")
elif topic in ['min_area_px', 'max_area_ratio', 'max_planarians', 'merge_kernel_size', 'min_contour_dist_px']:
value = int(value) if topic in ['min_area_px', 'max_planarians', 'merge_kernel_size', 'min_contour_dist_px'] else float(value)
self.manager.tracker_config[topic] = value
test_tube_scanner/scanner/static/scanner/js/calibration.js
+2 -1
View File
@@ -48,6 +48,7 @@ class ScannerManager {
this.max_planarians = options.max_planarians;
this.merge_kernel_size = options.merge_kernel_size;
this.min_contour_dist_px = options.min_contour_dist_px;
this.track = options.track;
}
@@ -84,7 +85,7 @@ class ScannerManager {
this.max_planarians.addEventListener('change', (e) => { this._send({ type: 'calibrate', topic: "max_planarians", value: e.target.value}); });
this.merge_kernel_size.addEventListener('change', (e) => { this._send({ type: 'calibrate', topic: "merge_kernel_size", value: e.target.value}); });
this.min_contour_dist_px.addEventListener('change', (e) => { this._send({ type: 'calibrate', topic: "min_contour_dist_px", value: e.target.value }); });
this.track.addEventListener('click', (e) => { this._send({ type: 'calibrate', topic: "track", value: e.target.value }); });
}
registerSocket(socket) {
test_tube_scanner/scanner/templates/scanner/calibration.html
+5 -2
View File
@@ -150,7 +150,9 @@
</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">{% trans 'Configuration du tracking' %}</div>
<div class="w3-col"><input id="_track" type="checkbox" value="0" onclick="if (this.checked){this.value='1';}else{ this.value='0';}">
{% trans 'Configuration du tracking' %}
</div>
<div class="w3-half">
<input id="_min_area_px" type="number" min="5" max="100" step="1" class="w3-round" value="{{ conf.min_area_px }}"
title="{% trans 'surface minimale de contour pour être considéré valide (px carré)' %}"><br>{% trans 'Min contour' %}
@@ -257,7 +259,8 @@
max_area_ratio : sId("_max_area_ratio"),
max_planarians : sId("_max_planarians"),
merge_kernel_size : sId("_merge_kernel_size"),
min_contour_dist_px : sId("_min_contour_dist_px")
min_contour_dist_px : sId("_min_contour_dist_px"),
track : sId("_track")
};
</script>
<script src="/static/scanner/js/calibration.js"></script>