Thank you for your advice.
I tried your advice, and it didn't seems to help (assuming it was done correctly).
I also tried running "external" python3.9 with the environment from Slicer, and it worked.
I also tried running with the bin/PythonSlicer executable (that uses the slicer environment), and it worked.
I tried running the code in a different process (using multiprocessing) but it looks like slicer does not work with multiprocessing.
Thanks
Hi, thanks for your reply!
It works using a standalone python 3.9 environment outside of 3D Slicer
here is the list of packages comparison between the different environments:
package clean version slicer version
------------------------- --------------- ----------------
certifi 2024.8.30 2023.7.22
charset-normalizer 3.4.0 3.3.0
depthai 2.29.0.0 2.29.0.0
idna 3.10 3.4
numpy 2.0.2 1.26.1
packaging 24.2 23.2
pip 24.2 23.3
pyparsing 3.2.0 3.1.1
python-dateutil 2.9.0.post0 2.8.2
requests 2.32.3 2.31.0
retrying 1.3.4 1.3.4
scipy 1.13.1 1.11.3
setuptools 75.1.0 68.2.2
six 1.17.0 1.16.0
typing_extensions 4.12.2 4.8.0
urllib3 2.2.3 2.0.6
wheel 0.44.0 0.41.2
ConfigArgParse 1.7 N/A
Flask 3.0.3 N/A
Jinja2 3.1.4 N/A
MarkupSafe 3.0.2 N/A
PyYAML 6.0.2 N/A
Pygments 2.18.0 N/A
Werkzeug 3.0.6 N/A
addict 2.4.0 N/A
asttokens 3.0.0 N/A
attrs 24.2.0 N/A
blinker 1.9.0 N/A
click 8.1.7 N/A
comm 0.2.2 N/A
contourpy 1.3.0 N/A
cycler 0.12.1 N/A
dash 2.18.2 N/A
dash-core-components 2.0.0 N/A
dash-html-components 2.0.0 N/A
dash-table 5.0.0 N/A
decorator 5.1.1 N/A
exceptiongroup 1.2.2 N/A
executing 2.1.0 N/A
fastjsonschema 2.21.1 N/A
fonttools 4.55.3 N/A
importlib_metadata 8.5.0 N/A
importlib_resources 6.4.5 N/A
ipython 8.18.1 N/A
ipywidgets 8.1.5 N/A
itsdangerous 2.2.0 N/A
jedi 0.19.2 N/A
joblib 1.4.2 N/A
jsonschema 4.23.0 N/A
jsonschema-specifications 2024.10.1 N/A
jupyter_core 5.7.2 N/A
jupyterlab_widgets 3.0.13 N/A
kiwisolver 1.4.7 N/A
matplotlib 3.9.4 N/A
matplotlib-inline 0.1.7 N/A
nbformat 5.10.4 N/A
nest-asyncio 1.6.0 N/A
open3d 0.18.0 N/A
opencv-python 4.10.0.84 N/A
pandas 2.2.3 N/A
parso 0.8.4 N/A
pexpect 4.9.0 N/A
pillow 11.0.0 N/A
platformdirs 4.3.6 N/A
plotly 5.24.1 N/A
prompt_toolkit 3.0.48 N/A
ptyprocess 0.7.0 N/A
pure_eval 0.2.3 N/A
pyquaternion 0.9.9 N/A
pytz 2024.2 N/A
referencing 0.35.1 N/A
rpds-py 0.22.3 N/A
scikit-learn 1.6.0 N/A
stack-data 0.6.3 N/A
tenacity 9.0.0 N/A
threadpoolctl 3.5.0 N/A
tqdm 4.67.1 N/A
traitlets 5.14.3 N/A
tzdata 2024.2 N/A
wcwidth 0.2.13 N/A
widgetsnbextension 4.0.13 N/A
zipp 3.21.0 N/A
CouchDB N/A 1.2
Deprecated N/A 1.2.14
GitPython N/A 3.1.37
Pillow N/A 10.1.0
PyGithub N/A 2.1.1
PyJWT N/A 2.8.0
PyNaCl N/A 1.5.0
SimpleITK N/A 2.2.1rc2.dev4
cffi N/A 1.16.0
chardet N/A 5.2.0
cryptography N/A 41.0.4
debugpy N/A 1.8.9
dicomweb-client N/A 0.59.1
gitdb N/A 4.0.10
pycparser N/A 2.21
pydicom N/A 2.4.3
smmap N/A 5.0.1
vtk N/A 9.2.20230607
wrapt N/A 1.15.0Hi,
I have a simple code that creates a pipeline that captures both L+R mono images and the disparity map, using OAK-D SR module.
This code works perfectly when running from python3.10 environment (Distro: Linux Mint 21.3 Virginia base: Ubuntu 22.04 jammy).
When I am running the code within 3D slicer scripted module environment (python 3.9), the same pipeline is stuck in the creation (dai.Device(pipeline)).
This is the debug dump I get when there is a successful run:
[2024-12-12 22:18:15.973] [depthai] [debug] Python bindings - version: 2.29.0.0 from build: 2024-11-24 09:54:26 +0000
[2024-12-12 22:18:15.973] [depthai] [debug] Library information - version: 2.29.0, commit: d6a37a5ba8ba2ee187fabc9208b813db5f75d4a7 from 2024-11-22 15:48:55 +0100, build: 2024-11-24 09:39:00 +0000, libusb enabled: true
[2024-12-12 22:18:15.978] [depthai] [debug] Initialize - finished
[2024-12-12 22:18:16.094] [depthai] [debug] Resources - Archive 'depthai-bootloader-fwp-0.0.28.tar.xz' open: 3ms, archive read: 116ms
[2024-12-12 22:18:16.643] [depthai] [debug] Resources - Archive 'depthai-device-fwp-4d360b5c56225f23e9a3d3a3999ce46c90cfdeaf.tar.xz' open: 2ms, archive read: 666ms
/home/ajax/dev/cflow/cflow_slicer_ext/cflow_pc/point_cloud/test_camera_depth_post_processing.py:43: DeprecationWarning: HIGH_DENSITY is deprecated, will be removed in future releases and replaced with DEFAULT.
depth.setDefaultProfilePreset(dai.node.StereoDepth.PresetMode.HIGH_DENSITY)
[2024-12-12 22:18:20.538] [host] [debug] Device - OpenVINO version: universal
[14442C101130B1D200] [3.2] [1734034700.538] [host] [debug] Device - BoardConfig: {"camera":[],"emmc":null,"gpio":[],"imu":null,"logDevicePrints":null,"logPath":null,"logSizeMax":null,"logVerbosity":null,"network":{"mtu":0,"xlinkTcpNoDelay":true},"nonExclusiveMode":false,"pcieInternalClock":null,"sysctl":[],"uart":[],"usb":{"flashBootedPid":63037,"flashBootedVid":999,"manufacturer":"","maxSpeed":4,"pid":63035,"productName":"","vid":999},"usb3PhyInternalClock":null,"uvc":null,"watchdogInitialDelayMs":null,"watchdogTimeoutMs":null}
libnop:
0000: b9 12 b9 07 81 e7 03 81 3b f6 81 e7 03 81 3d f6 04 bd 00 bd 00 b9 02 00 01 ba 00 be be bb 00 bb
0020: 00 be be be be be be be 00 bb 00 be be
[2024-12-12 22:18:21.508] [depthai] [debug] Searching for booted device: DeviceInfo(name=3.2, mxid=14442C101130B1D200, X_LINK_BOOTED, X_LINK_USB_VSC, X_LINK_MYRIAD_X, X_LINK_SUCCESS), name used as hint only
[14442C101130B1D200] [3.2] [1.270] [system] [info] Memory Usage - DDR: 0.12 / 333.26 MiB, CMX: 2.04 / 2.50 MiB, LeonOS Heap: 7.50 / 81.70 MiB, LeonRT Heap: 2.89 / 39.87 MiB / NOC ddr: 25 MB/s
[14442C101130B1D200] [3.2] [1.270] [system] [info] Temperatures - Average: 31.22C, CSS: 32.73C, MSS 30.56C, UPA: 30.56C, DSS: 31.04C
…
When Running within the 3D slicer, I get the following debug dump:
[2024-12-12 22:29:03.376] [depthai] [debug] Python bindings - version: 2.29.0.0 from build: 2024-11-24 09:50:04 +0000
[2024-12-12 22:29:03.376] [depthai] [debug] Library information - version: 2.29.0, commit: d6a37a5ba8ba2ee187fabc9208b813db5f75d4a7 from 2024-11-22 15:48:55 +0100, build: 2024-11-24 09:39:00 +0000, libusb enabled: true
[2024-12-12 22:29:03.380] [depthai] [debug] Initialize - finished
[2024-12-12 22:29:17.994] [host] [debug] Device - OpenVINO version: universal
[14442C101130B1D200] [3.2] [1734035357.995] [host] [debug] Device - BoardConfig: {"camera":[],"emmc":null,"gpio":[],"imu":null,"logDevicePrints":null,"logPath":null,"logSizeMax":null,"logVerbosity":null,"network":{"mtu":0,"xlinkTcpNoDelay":true},"nonExclusiveMode":false,"pcieInternalClock":null,"sysctl":[],"uart":[],"usb":{"flashBootedPid":63037,"flashBootedVid":999,"manufacturer":"","maxSpeed":4,"pid":63035,"productName":"","vid":999},"usb3PhyInternalClock":null,"uvc":null,"watchdogInitialDelayMs":null,"watchdogTimeoutMs":null}
libnop:
0000: b9 12 b9 07 81 e7 03 81 3b f6 81 e7 03 81 3d f6 04 bd 00 bd 00 b9 02 00 01 ba 00 be be bb 00 bb
0020: 00 be be be be be be be 00 bb 00 be be
The sample code is below (stuck on the last line):
# Closer-in minimum depth, disparity range is doubled (from 95 to 190):
extended_disparity = False
# Better accuracy for longer distance, fractional disparity 32-levels:
subpixel = False
# Better handling for occlusions:
lr_check = False
# Create pipeline
pipeline = dai.Pipeline()
# Define sources and outputs
monoLeft = pipeline.create(dai.node.MonoCamera)
monoRight = pipeline.create(dai.node.MonoCamera)
depth = pipeline.create(dai.node.StereoDepth)
xout = pipeline.create(dai.node.XLinkOut)
sync = pipeline.create(dai.node.Sync)
xout.setStreamName("disparity")
xout_01 = pipeline.create(dai.node.XLinkOut)
xout_01.input.setBlocking(False)
xout_01.setStreamName("mono")
# Properties
monoLeft.setResolution(dai.MonoCameraProperties.SensorResolution.THE_800_P)
monoLeft.setFps(10)
monoLeft.setCamera("left")
monoRight.setResolution(dai.MonoCameraProperties.SensorResolution.THE_800_P)
monoRight.setCamera("right")
monoLeft.setFps(10)
# Create a node that will produce the depth map (using disparity output as it's easier to visualize depth this way)
depth.setDefaultProfilePreset(dai.node.StereoDepth.PresetMode.HIGH_DENSITY)
depth.setLeftRightCheck(lr_check)
depth.setExtendedDisparity(extended_disparity)
depth.setSubpixel(subpixel)
config = depth.initialConfig.get()
config.postProcessing.median = dai.MedianFilter.KERNEL_7x7
config.postProcessing.speckleFilter.enable = True
config.postProcessing.speckleFilter.speckleRange = 10
config.postProcessing.temporalFilter.enable = False
config.postProcessing.spatialFilter.enable = True
config.postProcessing.spatialFilter.holeFillingRadius = 20
config.postProcessing.spatialFilter.numIterations = 1
config.postProcessing.thresholdFilter.minRange = 0
config.postProcessing.thresholdFilter.maxRange = 10000
config.postProcessing.decimationFilter.decimationFactor = 1
depth.initialConfig.set(config)
# Linking
monoLeft.out.link(depth.left)
monoLeft.out.link(sync.inputs['rgb'])
monoRight.out.link(depth.right)
depth.disparity.link(xout.input)
monoLeft.out.link(xout_01.input)
# Connect to device and start pipeline
with dai.Device(pipeline) as device:Thank you for your help.