Clean up useless files
This commit is contained in:
thibaut pollina
parent
52a538d742
commit
60bdc3ede6
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@ -1,97 +0,0 @@
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#MANUAL CONFIGURATION
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#COPY PASTE LINE BY LINE
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#Update and upgrade you Pi
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sudo apt-get update -y && sudo apt-get full-upgrade -y
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sudo reboot now
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#Configure your Pi
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sudo raspi-config
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#Interfacing Options > Camera > Yes > OK
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#Interfacing Options > SSH > Yes > OK
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#Interfacing Options > I2C > Yes > OK
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#Interfacing Options > SSH > No > Yes > OK
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#Reboot > Yes
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#Install librairies for the steppers (pump and focus)
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pip3 install adafruit-blinka
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sudo pip3 install adafruit-circuitpython-motorkit
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#Install the librairy for the fan
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git clone https://github.com/WiringPi/WiringPi.git
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cd WiringPi
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sudo ./build
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sudo apt-get install gcc -y
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#Install Node-Red
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cd
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sudo apt-get install build-essential -y
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bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered)
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#Press y and y again to confirm the installation of Node-RED and wait.
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cd .node-red/
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npm install node-red-dashboard
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npm install node-red-contrib-python3-function
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npm install node-red-contrib-camerapi
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npm install node-red-contrib-gpsd
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npm install node-red-contrib-web-worldmap
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sudo systemctl enable nodered.service
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#BUILD CONFIGURATION
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#COPY PASTE BLOCK BY BLOCK
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sudo pip3 install jupyter
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pip install matplotlib
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pip3 install matplotlib
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sudo apt-get install exfat-fuse -y
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sudo apt-get install exfat-utils -y
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pip install paho-mqtt
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pip3 install paho-mqtt
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sudo apt-get install mosquitto mosquitto-clients -y
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pip install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
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pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
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sudo pip3 install morphocut --upgrade
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pip3 install morphocut --upgrade
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pip3 uninstall morphocut
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pip uninstall morphocut
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pip uninstall -U git+https://github.com/morphocut/morphocut.git@pyrocystis
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pip freeze | xargs pip uninstall -y
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pip3 freeze | xargs pip3 uninstall -y
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sudo pip3 freeze | xargs pip3 uninstall -y
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pip3 uninstall morphocut
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sudo pip3 uninstall morphocut
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sudo pip3 install morphocut
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sudo pip3 uninstall morphocut
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pip install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
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pip3 install -U git+https://github.com/morphocut/morphocut.git@pyrocystis
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sudo apt-get purge wolfram-engine -y
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sudo apt-get remove vlc* -y
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sudo apt-get update -y && sudo apt-get upgrade -y
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sudo apt-get install build-essential cmake pkg-config -y
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sudo apt-get install libjpeg-dev libtiff5-dev libjasper-dev libpng12-dev -y
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sudo apt-get install libavcodec-dev libavformat-dev libswscale-dev libv4l-dev -y
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sudo apt-get install libxvidcore-dev libx264-dev -y
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sudo apt-get install libgtk2.0-dev -y
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sudo apt-get install libatlas-base-dev gfortran -y
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sudo apt-get install python2.7-dev python3-dev -y
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sudo apt-get install libjpeg-dev libtiff5-dev libjasper-dev libpng-dev -y
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sudo apt-get install libfontconfig1-dev libcairo2-dev -y
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sudo apt-get install libgdk-pixbuf2.0-dev libpango1.0-dev -y
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sudo apt-get install libgtk2.0-dev libgtk-3-dev -y
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sudo apt-get install libhdf5-dev libhdf5-serial-dev libhdf5-103 -y
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sudo apt-get install libqtgui4 libqtwebkit4 libqt4-test python3-pyqt5 -y
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pip install "picamera[array]"
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pip3 install opencv-contrib-python==4.1.0.25
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sudo apt-get install ffmpeg git python3-picamera python3-ws4py -y
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git clone https://github.com/waveform80/pistreaming.git
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git clone git@github.com:Lawouach/WebSocket-for-Python.git
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pip install ws4py
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pip3 install ws4py
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pip3 install pyzmq
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@ -1,72 +0,0 @@
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#test using python3.7 morphocut.py
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Processing images under /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15...
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0it [00:00, ?it/s]
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0it [00:00, ?it/s]Found 94 files in /home/pi/Desktop/PlanktonScope_acquisition/01_16_2020/15.
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Object 35_41_180124_84: : 85it [00:17, 5.95it/s]
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Frame 35_41_180124: : 1it [00:17, 17.03s/it]
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Object 35_41_763395_168: : 169it [00:24, 47.97it/s]
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Frame 35_41_763395: : 2it [00:24, 14.11s/it]
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Object 35_42_339153_245: : 245it [00:31, 44.73it/s]
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Frame 35_42_339153: : 3it [00:31, 11.93s/it]
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Object 35_42_899894_320: : 319it [00:38, 42.28it/s]
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Frame 35_42_899894: : 4it [00:38, 10.44s/it]
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Object 35_43_467613_394: : 394it [00:45, 44.59it/s]
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Frame 35_43_467613: : 5it [00:44, 9.36s/it]
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Object 35_44_040639_465: : 466it [00:56, 32.28it/s]
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Frame 35_44_040639: : 6it [00:59, 9.95s/it]
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Object 35_44_040639_465: : 466it [00:59, 7.78it/s]
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Traceback (most recent call last):
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File "/home/pi/Downloads/Morphocut.py", line 115, in <module>
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p.run()
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 748, in run
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for _ in self.transform_stream():
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
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for obj in progress:
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File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
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for obj in iterable:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/contrib/ecotaxa.py", line 111, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 184, in transform_stream
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for i, obj in enumerate(stream, start=self.start):
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 142, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/stream.py", line 68, in transform_stream
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for obj in progress:
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File "/home/pi/.local/lib/python3.7/site-packages/tqdm/std.py", line 1104, in __iter__
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for obj in iterable:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 489, in transform_stream
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for obj in stream:
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/core.py", line 492, in transform_stream
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result = self.transform(*parameters) # pylint: disable=no-member
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File "/home/pi/.local/lib/python3.7/site-packages/morphocut/image.py", line 78, in transform
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image, in_range=in_range, out_range=self.out_range
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File "/home/pi/.local/lib/python3.7/site-packages/skimage/exposure/exposure.py", line 352, in rescale_intensity
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image = (image - imin) / float(imax - imin)
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MemoryError
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#!/usr/bin/env python
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from adafruit_motor import stepper
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from adafruit_motorkit import MotorKit
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from time import sleep
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from thread2 import Thread
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import sys
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nb_step = int(sys.argv[1])
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orientation = str(sys.argv[2])
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toogler = str(sys.argv[3])
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#Execute a python cmd with the previous defined variables from php
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kit = MotorKit()
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stage = kit.stepper1
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stage.release()
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def focus(steps,orientation):
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#0.25mm/step
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#31um/microsteps
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stage.release()
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if orientation == 'up':
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for i in range(steps):
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stage.onestep(direction=stepper.FORWARD, style=stepper.MICROSTEP)
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sleep(0.001)
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if orientation == 'down':
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for i in range(steps):
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stage.onestep(direction=stepper.BACKWARD, style=stepper.MICROSTEP)
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sleep(0.001)
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stage.release()
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focus_thread = Thread(target = focus, name = 'focus_thread', args =(nb_step, orientation) )
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if toogler == "ON":
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focus_thread.start()
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focus_thread.isAlive()
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if toogler == "OFF":
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focus_thread.terminate()
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focus_thread.join()
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focus_thread.isAlive()
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stage.release()
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@ -1,41 +0,0 @@
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from adafruit_motor import stepper
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from adafruit_motorkit import MotorKit
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from time import sleep
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import sys
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vol = int(sys.argv[1])
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flowrate = float(sys.argv[2])
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dir = str(sys.argv[3])
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kit = MotorKit()
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pump_stepper = kit.stepper2
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pump_stepper.release()
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def pump(vol, flowrate, dir):
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if dir == "foward":
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dir=stepper.FORWARD
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if dir == "backward":
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dir=stepper.BACKWARD
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nb_step=vol*507 #if sleep(0.05) in between 2 steps
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#35000steps for 69g
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#nb_step=vol*460 if sleep(0) in between 2 steps
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duration=(vol*60)/flowrate
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delay=(duration/nb_step)-0.005
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for i in range(nb_step):
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pump_stepper.onestep(direction=dir, style=stepper.DOUBLE)
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sleep(delay)
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sleep(1)
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pump_stepper.release()
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#volume, flowrate (from 0 to 20), direction (foward or backward)
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pump(vol, flowrate, dir)
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@ -1,9 +0,0 @@
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cd ~
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sudo touch starting.sh
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sudo chmod 777 starting.sh
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sudo echo 'sudo chmod 777 /dev/i2c-1' >> starting.sh
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sudo echo './starting.sh' >> .bashrc
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sudo reboot
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Binary file not shown.
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@ -1,11 +0,0 @@
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#!/bin/bash
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#In order to kill an on going acquisition, type this command
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#bash $HOME/PlanktonScope/scripts/kill_image.sh image.py in_path sample_project sample_id acq_id
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path=$1
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kill -9 `ps ax | grep "image.py" | head -1 | awk '{print $1}'`
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kill -9 `ps ax | grep "image.py" | head -1 | awk '{print $1}'`
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rm -r $path
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#!/bin/bash
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#Run this script using this type of command line : bash killer.sh name_of_the_python_script_to_kill.py
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scrip_name=$1
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kill -9 `ps ax | grep "$scrip_name" | head -1 | awk '{print $1}'`
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python3.7 $HOME/PlanktonScope/scripts/recover.py
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