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.. _install: .. _install:
============ ==========================
Installation PlanktonScope Installation
============ ==========================
.. _raspbian_install:
Python Installation of MotorKit Library pi@raspberrypi:~/retext $ python3 retext.py
=======================================
https://learn.adafruit.com/adafruit-dc-and-stepper-motor-hat-for-raspberry-pi/installing-software
Adafruit Ultimate GPS HAT Installation Install Raspbian on your Raspberry Pi
====================================== Download the image
https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi?view=all Download the .zip file of Raspbian Buster with desktop from the Raspberry Pi website Downloads page.
MorphoCut Installation Writing an image to the SD card
====================== Download the latest version of balenaEtcher and install it.
https://morphocut.readthedocs.io/en/stable/installation.html Connect an SD card reader with the micro SD card inside.
Open balenaEtcher and select from your hard drive the Raspberry Pi .zip file you wish to write to the SD card.
Select the SD card you wish to write your image to.
Review your selections and click 'Flash!' to begin writing data to the SD card.
RPi Cam Web Interface Installation Prepare your Raspberry Pi
================================== https://projects.raspberrypi.org/en/projects/raspberry-pi-getting-started/
Plug the SD Card in your Raspberry Pi
Connect your Pi to a screen, mouse, keyboard and power
Finish the setup
Install the needed libraries for the PlanktonScope
Make sure you have access to internet and update/upgrade your fresh raspbian
Update your Pi first::
sudo apt-get update -y
sudo apt-get upgrade -y
Reboot your Pi safely::
sudo reboot now
Install CircuitPython
https://learn.adafruit.com/circuitpython-on-raspberrypi-linux/installing-circuitpython-on-raspberry-pi
Type this command::
sudo apt-get install python3-pip
Enable I2C and SPI
A vast number of our CircuitPython drivers use I2C and SPI for interfacing so you'll want to get those enabled.
You only have to do this once per Raspberry Pi but by default both interfaces are disabled!
Enable I2C
Enable SPI
Once you're done with both::
sudo reboot now
Verify you have the I2C and SPI devices with the command::
ls /dev/i2c* /dev/spi*
Run the following command to install adafruit_blinka::
pip3 install adafruit-blinka
Install MotorKit
https://learn.adafruit.com/adafruit-dc-and-stepper-motor-hat-for-raspberry-pi?view=all
Check I2C it is working::
i2cdetect -y 1
Install Circuit Python::
sudo pip3 install adafruit-circuitpython-motorkit
Install RPi Cam Web Interface
https://elinux.org/RPi-Cam-Web-Interface https://elinux.org/RPi-Cam-Web-Interface
Attach the PiCamera to your Raspberry Pi
Enable Camera/SSH/I2C in raspi-config::
sudo raspi-config
Reboot::
sudo reboot now
Update your RPi::
sudo apt-get update -y
sudo apt-get upgrade -y
Reboot your Pi safely::
sudo reboot now
Clone the code from github and enable and run the install script with the following commands::
git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git
cd RPi_Cam_Web_Interface
./install.sh
Press Enter to allow default setting of the installation
Press Enter to start RPi Cam Web Interface now
Found what is the IP of your Raspberry Pi::
sudo ip addr show | grep 'inet 1'
Reach the url on a local browser : http://127.0.0.1/html/
Install Ultimate GPS HAT
Set up the Pi to release the console pins
https://learn.adafruit.com/adafruit-ultimate-gps-hat-for-raspberry-pi/pi-setup
Run sudo raspi-config to open up the configuration page and select Interfacing Options :
Select Serial
Select NO
Keep the Serial Port Hardware enabled
Thats it!
Shutdown your Pi safely::
sudo shutdown -h now
http://www.danmandle.com/blog/getting-gpsd-to-work-with-python/
Install RGB Cooling HAT
https://www.yahboom.net/study/RGB_Cooling_HAT
https://github.com/YahboomTechnology/Raspberry-Pi-RGB-Cooling-HAT
Type this command::
git clone https://github.com/WiringPi/WiringPi.git
cd WiringPi
sudo ./build
sudo apt-get install gcc
Download temp_control.zip::
Unzip it in /home/pi/
cd temp_control/
Uncomment all lines related to I2C led
//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x03);
//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x04);
//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x02);
//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x01);
//wiringPiI2CWriteReg8(fd_i2c, 0x04, 0x03);
gcc -o temp_control temp_control.c ssd1306_i2c.c -lwiringPi
Install Node-RED
https://nodered.org/docs/getting-started/raspberrypi
Type this command::
bash <(curl -sL https://raw.githubusercontent.com/node-red/linux-installers/master/deb/update-nodejs-and-nodered)
Raspbian installation
=====================
If you are using the `Raspbian`_ distro, it is best to install picamera using
the system's package manager: apt. This will ensure that picamera is easy to
keep up to date, and easy to remove should you wish to do so. It will also make
picamera available for all users on the system. To install picamera using apt
simply::
$ sudo apt-get update
$ sudo apt-get install python-picamera python3-picamera
To upgrade your installation when new releases are made you can simply use
apt's normal upgrade procedure::
$ sudo apt-get update
$ sudo apt-get upgrade
If you ever need to remove your installation::
$ sudo apt-get remove python-picamera python3-picamera
.. note::
If you are using a recent installation of Raspbian, you may find that the
python-picamera package is already installed (it is included by default
in recent versions).
.. _Raspbian: http://www.raspbian.org/
.. _non_raspbian_install:
Alternate distro installation Install MorphoCut
============================= https://morphocut.readthedocs.io/en/stable/installation.html
MorphoCut is packaged on PyPI and can be installed with pip::
pip install morphocut
On distributions other than Raspbian, it is probably simplest to install system Install MorphoCut server
wide using Python's ``pip`` tool:: https://github.com/morphocut/morphocut-server
Morphocut server requires Docker Compose, Nodejs and Conda
Docker Compose
Installing Docker
https://withblue.ink/2019/07/13/yes-you-can-run-docker-on-raspbian.html
Installing Docker CE on Raspbian (Stretch or Buster) for Raspberry Pi is straightforward, and its fully supported by Docker. Docker CE is not supported on Raspbian Jessie anymore, so Id recommend upgrading to a more recent release.
Were going to install Docker from the official Docker repositories. While there are Docker packages on the Raspbian repos too, those are not kept up to date, which is something of an issue with a fast-evolving software like Docker.
To install Docker CE on Raspbian Stretch and Buster:
Install some required packages first
sudo apt update -y
sudo apt install -y apt-transport-https ca-certificates curl gnupg2 software-properties-common
$ sudo pip install picamera Get the Docker signing key for packages
curl -fsSL https://download.docker.com/linux/$(. /etc/os-release; echo "$ID")/gpg | sudo apt-key add -
If you wish to use the classes in the :mod:`picamera.array` module then specify Add the Docker official repos
the "array" option which will pull in numpy as a dependency (be warned that echo "deb [arch=armhf] https://download.docker.com/linux/$(. /etc/os-release; echo "$ID") \
building numpy takes a *long* time on a Pi):: $(lsb_release -cs) stable" | \
sudo tee /etc/apt/sources.list.d/docker.list
$ sudo pip install "picamera[array]" The aufs package, part of the "recommended" packages, won't install on Buster just yet, because of missing pre-compiled kernel modules. We can work around that issue by using "--no-install-recommends"
sudo apt update
sudo apt install -y --no-install-recommends \
docker-ce \
cgroupfs-mount
To upgrade your installation when new releases are made:: Thats it! The next step is about starting Docker and enabling it at boot:
sudo systemctl enable docker
sudo systemctl start docker
$ sudo pip install -U picamera Now that we have Docker running, we can test it by running the “hello world” image:
sudo docker run --rm arm32v7/hello-world
If you ever need to remove your installation:: If everything is working fine, the command above will output something similar to:
$ sudo pip uninstall picamera
.. _firmware:
Firmware upgrades About ARM images
================= This should hardly come as a surprise, but theres a caveat with running Docker on a Raspberry Pi. Since those small devices do not run on x86_64, but rather have ARM-based CPUs, you wont be able to use all the packages on the Docker Hub.
Instead, you need to look for images distributed by the arm32v7 organization (called armhf before), or tagged with those labels. Good news is that the arm32v7 organization is officially supported by Docker, so you get high-quality images.
While the CPUs inside Raspberry Pi 3s and 4s are using the ARMv8 (or ARM64) architecture, Raspbian is compiled as a 32-bit OS, so using Raspbian youre not able to run 64-bit applications or containers.
Many common applications are already pre-built for ARM, including a growing number of official images, and you can also find a list of community-contributed arm32v7 images on Docker Hub. However, this is still a fraction of the number of images available for the x86_64 architecture.
Installing Docker Compose
In this last step were installing Docker Compose.
The official installation method for Linux, as in the Docker documentation, points users to the GitHub downloads page, which however does not offer pre-built binaries for the ARM architecture.
Luckily, we can still easily install Docker Compose from pip:
Install required packages
sudo apt update
sudo apt install -y python python-pip libffi-dev python-backports.ssl-match-hostname
The behaviour of the Pi's camera module is dictated by the Pi's firmware. Over Install Docker Compose from pip, this might take a while :
time, considerable work has gone into fixing bugs and extending the sudo pip install docker-compose
functionality of the Pi's camera module through new firmware releases. Whilst
the picamera library attempts to maintain backward compatibility with older Pi
firmwares, it is only tested against the latest firmware at the time of
release, and not all functionality may be available if you are running an older
firmware. As an example, the :attr:`~PiCamera.annotate_text` attribute relies
on a recent firmware; older firmwares lacked the functionality.
You can determine the revision of your current firmware with the following With this, you now have a complete Raspberry Pi mini-server running Docker and ready to accept your containers.
command:: Nodejs
https://www.instructables.com/id/Install-Nodejs-and-Npm-on-Raspberry-Pi/
Conda
https://stackoverflow.com/questions/39371772/how-to-install-anaconda-on-raspberry-pi-3-model-b
Go and get the latest version of miniconda for Raspberry Pi - made for armv7l processor and bundled with Python 3 (eg.: uname -m)
wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh
md5sum Miniconda3-latest-Linux-armv7l.sh
bash Miniconda3-latest-Linux-armv7l.sh
$ uname -a After installation, source your updated .bashrc file with :
source ~/.bashrc
The firmware revision is the number after the ``#``:: Then enter the command,
python --version
Linux kermit 3.12.26+ #707 PREEMPT Sat Aug 30 17:39:19 BST 2014 armv6l GNU/Linux which should give you :
/ Python 3.4.3 :: Continuum Analytics, Inc.
/
firmware revision --+
On Raspbian, the standard upgrade procedure should keep your firmware Install Jupyter Notebook
up to date:: https://www.instructables.com/id/Jupyter-Notebook-on-Raspberry-Pi/
sudo su -
apt-get update
apt-get install python3-matplotlib
apt-get install python3-scipy
pip3 install --upgrade pip
reboot
sudo pip3 install jupyter
$ sudo apt-get update Script to realize an acquisition
$ sudo apt-get upgrade Set color FAN HAT to init
Get a fix
Set the pump to fast for x seconds
Set the pump to super slow
Set the focus manually
Click on start
Set the pump to normal flowrate
Set the picamera
.. warning:: Bill of Material
Items
Previously, these documents have suggested using the ``rpi-update`` utility Quantity
to update the Pi's firmware; this is now discouraged. If you have Price
previously used the ``rpi-update`` utility to update your firmware, you can µ-Slide I Luer Variety Pack
switch back to using ``apt`` to manage it with the following commands:: 1
$120
$ sudo apt-get update M12 Lens Set
$ sudo apt-get install --reinstall libraspberrypi0 libraspberrypi-{bin,dev,doc} raspberrypi-bootloader 1
$ sudo rm /boot/.firmware_revision $60
Raspberry Pi 4 Model B
You will need to reboot after doing so. 1
$62
.. note:: Peristaltic Metering Pump with Stepper Motor
1
Please note that the `PiTFT`_ screen (and similar GPIO-driven screens) $60
requires a custom firmware for operation. This firmware lags behind the Adafruit Ultimate GPS HAT Needs the antenna
official firmware and at the time of writing lacks several features 1
including long exposures and text overlays. $43
Adapter RMS to M12 x 0.5
.. _PiTFT: http://www.adafruit.com/product/1601 1
$42
MicroSD Card 256GB
1
$28
Adafruit DC & Stepper Motor HAT
1
$27
Raspberry Pi Camera Module V2
1
$25
Linear Stepper Motor 12V Focus actuators
2
$20
Yahboom Cooling Fan Hat
1
$17
Adafruit GPS Antenna
1
$15
Power Supply 12V 2A
1
$10
Adafruit Power Supply 5.1V 3A - USB C
1
$10
Adafruit Hammer Header Male
1
$7
Adafruit GPIO Ribbon Cable
1
$3
Adafruit GPIO Stacking Header
1
$2
Female Mount Connector Jack Socket
1
$1
Switch Accessory, RJ45 Socket
1
$1
Standoff Male to Female 6mm - 2.5mm
8
$1
White LED 5mm Ultra Bright
1
$0
Standoff Male to Female 15mm - 2.5mm
8
$0
Machine Screw, M2.5
8
$0
6mm thick acrylic - 60cm x 30cm
1
$0
.. _dev_install:
Development installation
========================
If you wish to develop picamera itself, it is easiest to obtain the source by
cloning the GitHub repository and then use the “develop” target of the Makefile
which will install the package as a link to the cloned repository allowing
in-place development (it also builds a tags file for use with vim/emacs with
Exuberants ctags utility). The following example demonstrates this method
within a virtual Python environment::
$ sudo apt-get install lsb-release build-essential git git-core \
exuberant-ctags python-virtualenv python3-virtualenv python-dev \
python3-dev libjpeg8-dev zlib1g-dev libav-tools \
texlive-latex-recommended texlive-latex-extra texlive-fonts-recommended
$ virtualenv -p /usr/bin/python3 sandbox
$ source sandbox/bin/activate
(sandbox) $ git clone https://github.com/waveform80/picamera.git
(sandbox) $ cd picamera
(sandbox) $ make develop
To pull the latest changes from git into your clone and update your
installation::
$ source sandbox/bin/activate
(sandbox) $ cd picamera
(sandbox) $ git pull
(sandbox) $ make develop
To remove your installation blow away the sandbox and the clone::
$ rm -fr ~/sandbox/ ~/picamera/
For anybody wishing to hack on the project, I would strongly recommend reading
through the :class:`PiCamera` class' source, to get a handle on using the
``mmalobj`` layer. This is a layer introduced in picamera 1.11 to ease the
usage of ``libmmal`` (the underlying library that picamera, ``raspistill``,
and ``raspivid`` all rely upon).
Beneath ``mmalobj`` is a :mod:`ctypes` translation of the ``libmmal`` headers
but my hope is that most developers will never need to deal with this
directly (thus, a working knowledge of C is hopefully no longer necessary to
hack on picamera).
Various classes for specialized applications also exist
(:class:`PiCameraCircularIO`, :class:`~array.PiBayerArray`, etc.)
Even if you dont feel up to hacking on the code, Id love to hear suggestions
from people of what youd like the API to look like (even if the code itself
isnt particularly pythonic, the interface should be)!
.. _test_suite:
Test suite sudo apt-get update -y
==========
If you wish to run the picamera test suite, follow the instructions in sudo apt-get upgrade -y
:ref:`dev_install` above and then make the "test" target within the sandbox::
$ source sandbox/bin/activate sudo apt-get install gpsd gpsd-clients python-gps
(sandbox) $ cd picamera -> not installed ion python3.7
(sandbox) $ make test pip3 install gps
.. warning::
The test suite takes a *very* long time to execute (at least 1 hour on an //test to add the tiny HQ clock (useless if the GPS works)
overclocked Pi 3). Depending on configuration, it can also lockup the sudo apt-get install gcc
camera requiring a reboot to reset, so ensure you are familiar with SSH or
using alternate TTYs to access a command line in the event you need to git clone https://github.com/silvanmelchior/RPi_Cam_Web_Interface.git
reboot. cd RPi_Cam_Web_Interface/
./install.sh
./stop.sh
sudo pip3 install adafruit-circuitpython-motorkit
pip install morphocut
-> Could not find a version that satisfies the requirement morphocut (from versions: )
No matching distribution found for morphocut
pip3 install morphocut
-> not installed properly - Read timed out
sudo pip3 install morphocut
-> need a better internet
install morphocut server
wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-armv7l.sh
sudo md5sum Miniconda3-latest-Linux-armv7l.sh
acq_autoimage_rate
acq_camera_name
acq_celltype
acq_dsp_firmware
acq_end
acq_flash_delay
acq_flash_duration
acq_flow_cell_type
acq_fluid_volume_imaged
acq_id
acq_initialization
acq_instrument
acq_magnification
acq_max_esd
acq_min_esd
acq_mode
acq_raw_image_total
acq_recalibration_interval_minute
acq_sampling_time
acq_save_image_file
acq_serialno
acq_software
acq_start
acq_stop_reason
acq_threshold_black
Acq_threshold_light
object_%area
object_angle
object_area
object_area_exc
object_bx
object_by
object_cdexc
object_centroids
object_circ.
object_circex
object_compentropy
object_compm1
object_compm2
object_compm3
object_compmean
object_compslope
object_convarea
object_convarea_area
object_convperim
object_convperim_perim
object_cv
object_date
object_depth_max
object_depth_min
object_elongation
object_esd
object_fcons
object_feret
object_feretareaexc
object_fractal
object_height
object_histcum1
object_histcum2
object_histcum3
object_id
object_intden
object_kurt
object_kurt_mean
object_lat
object_link
object_lon
object_major
object_max
object_mean
object_meanimagegrey
object_meanpos
object_median
object_median_mean
object_median_mean_range
object_min
object_minor
object_mode
object_nb1
object_nb1_area
object_nb1_range
object_nb2
object_nb2_area
object_nb2_range
object_nb3
object_nb3_area
object_nb3_range
object_perim.
object_perimareaexc
object_perimferet
object_perimmajor
object_range
object_skelarea
object_skeleton_area
object_skew
object_skew_mean
object_slope
object_sr
object_stddev
object_symetrieh
object_symetrieh_area
object_symetriehc
object_symetriev
object_symetriev_area
object_symetrievc
object_tag
object_thickr
object_time
object_width
object_x
object_xm
object_xmg5
object_xstart
object_y
object_ym
object_ymg5
object_ystart
process_background_method
process_esd_max
process_esd_min
process_gamma_value
process_grey_auto_adjust
process_id
process_lut_offset
process_lut_slope
process_nb_images
process_nb_of_rawfile_images_in_folder
process_objects_processed
process_pixel
process_remove_duplicates
process_remove_objects_on_sides
process_rolling
process_scale
process_software
process_start_date
process_start_time
process_stop_after_m_objects
process_stop_n_images
process_upper
sample_barcode
sample_comment_or_volume
sample_dataportal_descriptor
sample_filename
sample_id
sample_project
sample_samplinggear
sample_ship
sample_volconc
sample_volpump