Replace all references to PlanktoNScope by PlanktoScope

.github/workflows/auto-label.yml

@@ -19,7 +19,7 @@ jobs:
         contains(github.event.issue.labels.*.name, 'hardware') ||
         contains(github.event.pull_request.labels.*.name, 'hardware')
       with:
-        project: 'https://github.com/PlanktonPlanet/PlanktonScope/projects/2'
+        project: 'https://github.com/PlanktonPlanet/PlanktoScope/projects/2'
         column_name: 'Bugs'
 
     - name: Assign issues and pull requests with `software` label to project `Sofware`
@@ -28,5 +28,5 @@ jobs:
         contains(github.event.issue.labels.*.name, 'software') ||
         contains(github.event.pull_request.labels.*.name, 'software')
       with:
-        project: 'https://github.com/PlanktonPlanet/PlanktonScope/projects/1'
+        project: 'https://github.com/PlanktonPlanet/PlanktoScope/projects/1'
         column_name: 'To Do'

README.md

@@ -33,7 +33,7 @@ There are several ways to join the development effort, share your progress with
 
 We are using slack as a communication platform between interested parties. You can [request to join by filling this form](https://docs.google.com/forms/d/e/1FAIpQLSfcod-avpzWVmWj42_hW1v2mMSHm0DAGXHxVECFig2dnKHxGQ/viewform).
 
-This repository is also a good way to get involved. Please fill in an issue if you witnessed a bug in the software or hardware. If you are able, you can also join the development effort. Look through the [issues opened](https://github.com/PlanktonPlanet/PlanktonScope/labels/good%20first%20issue) and choose one that piques your interest. Let us know you want to work on it in the comments, we may even be able to guide your beginnings around the code.
+This repository is also a good way to get involved. Please fill in an issue if you witnessed a bug in the software or hardware. If you are able, you can also join the development effort. Look through the [issues opened](https://github.com/PlanktonPlanet/PlanktoScope/labels/good%20first%20issue) and choose one that piques your interest. Let us know you want to work on it in the comments, we may even be able to guide your beginnings around the code.
 
 # License: Our work is fully open source
 

config.json

@@ -6,7 +6,7 @@
     "sample_sampling_gear": "net",
     "sample_gear_net_opening": 40,
     "acq_id": 1,
-    "acq_instrument": "PlanktonScope v2.2",
+    "acq_instrument": "PlanktoScope v2.2",
     "acq_celltype": 200,
     "acq_minimum_mesh": 10,
     "acq_maximum_mesh": 200,

docs/easy_install.md

@@ -1,4 +1,4 @@
-# PlanktonScope Simple Setup Guide
+# PlanktoScope Simple Setup Guide
 
 ## Download the image
 
@@ -19,7 +19,7 @@ Review your selections and click 'Flash!' to begin writing data to the SD card.
 ## Inserting the SD card
 Once flashing is over, you can unmount the SD card from the computer (usually done by right clicking on the card icon in the taskbar).
 
-Insert now the card in the Raspberry installed in your PlanktonScope.
+Insert now the card in the Raspberry installed in your PlanktoScope.
 
 ## Install a mDNS client
 
@@ -33,4 +33,4 @@ To install the client, download the installer [here](https://download.info.apple
 
 ## Start playing!
 
-Start up your PlanktonScope and connect to its WiFi network. You can now access the webpage at http://planktonscope.local:1880/ui to start using your machine!
+Start up your PlanktoScope and connect to its WiFi network. You can now access the webpage at http://planktoscope.local:1880/ui to start using your machine!

docs/edit_the_code.md

@@ -2,7 +2,7 @@
 
 We are using the [Github Flow approach](https://docs.github.com/en/free-pro-team@latest/github/collaborating-with-issues-and-pull-requests) for our development efforts.
 
-If you want to join us, have a look at the [currently opened issues](https://github.com/PlanktonPlanet/PlanktonScope/issues) and pick one where you feel like you can have an impact. Let us know you want to work it in the comments and get started.
+If you want to join us, have a look at the [currently opened issues](https://github.com/PlanktonPlanet/PlanktoScope/issues) and pick one where you feel like you can have an impact. Let us know you want to work it in the comments and get started.
 
 For working on Node-Red, we recommend to install it directly on your development machine to allow for faster cycles of testing (and ease of use). But feel free to setup a Pi Zero as a portable and compact development environment! (One of us is using one configured as usb gadget to do so!)
 

docs/edit_this_doc.md

@@ -2,7 +2,7 @@
 
 This documentation is hosted by [ReadTheDocs.org](https://readthedocs.org/) at https://planktonscope.readthedocs.io/.
 
-The source files are in the main [github repository](https://www.github.com/PlanktonPlanet/PlanktonScope), in the `docs` folder.
+The source files are in the main [github repository](https://www.github.com/PlanktonPlanet/PlanktoScope), in the `docs` folder.
 
 They are simple [Markdown files](https://www.markdownguide.org/), that you can edit in any text editor of your choice.
 
@@ -12,7 +12,7 @@ After installing mkdocs, you can use `mkdocs serve` in the main folder of this r
 
 If you want to include pictures and diagrams in the documentation, please set the pictures in a dedicated folder to the name of the page you are creating (for example, if your page is named `expert_setup.md`, please put all the related pictures in the `docs/expert_setup/` folder). Each picture should be named with a simple yet descriptive name, using jpg or png format if possible. Try to limit the size of the file by limiting the resolution to what is necessary for the picture to be clear on screen.
 
-Contributions should be made by creating pull requests on [Github directly](https://github.com/PlanktonPlanet/PlanktonScope/pulls).
+Contributions should be made by creating pull requests on [Github directly](https://github.com/PlanktonPlanet/PlanktoScope/pulls).
 
 
 ## Extensions available

morphocut/README.md

@@ -1,221 +0,0 @@
-#########################################################
-Installation of MorphoCut development version:
-#########################################################
-
-$ pip install -U git+https://github.com/morphocut/morphocut.git
-Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
-Collecting git+https://github.com/morphocut/morphocut.git
-  Cloning https://github.com/morphocut/morphocut.git to /tmp/pip-req-build-NnGYk4
-  Installing build dependencies ... error
-  Complete output from command /usr/bin/python -m pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-e4DHrk --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple --extra-index-url https://www.piwheels.org/simple -- setuptools wheel:
-  Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple, https://www.piwheels.org/simple
-  Collecting setuptools
-    Downloading https://www.piwheels.org/simple/setuptools/setuptools-45.0.0-py2.py3-none-any.whl (583kB)
-  setuptools requires Python '>=3.5' but the running Python is 2.7.16
-  
-  ----------------------------------------
-Command "/usr/bin/python -m pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-e4DHrk --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple --extra-index-url https://www.piwheels.org/simple -- setuptools wheel" failed with error code 1 in None
-
-#########################################################
-Installation of MorphoCut packaged on PyPI via pip
-#########################################################
-
-$ pip install morphocut
-Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
-Collecting morphocut
-  Could not find a version that satisfies the requirement morphocut (from versions: )
-No matching distribution found for morphocut
-
-#########################################################
-Installation of MorphoCut packaged on PyPI via pip3
-#########################################################
-
-$ pip3 install morphocut
-Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
-Collecting morphocut
-  Downloading https://files.pythonhosted.org/packages/7e/c7/1addaf867234dd30db6d1f4bf8d3b685d93b743023a863814451abd5cef8/morphocut-0.1.1-py3-none-any.whl
-Collecting scikit-image>=0.16.0 (from morphocut)
-  Downloading https://www.piwheels.org/simple/scikit-image/scikit_image-0.16.2-cp37-cp37m-linux_armv7l.whl (39.7MB)
-    100% |████████████████████████████████| 39.7MB 10kB/s 
-Collecting tqdm (from morphocut)
-  Downloading https://files.pythonhosted.org/packages/72/c9/7fc20feac72e79032a7c8138fd0d395dc6d8812b5b9edf53c3afd0b31017/tqdm-4.41.1-py2.py3-none-any.whl (56kB)
-    100% |████████████████████████████████| 61kB 1.6MB/s 
-Collecting scipy (from morphocut)
-  Downloading https://files.pythonhosted.org/packages/04/ab/e2eb3e3f90b9363040a3d885ccc5c79fe20c5b8a3caa8fe3bf47ff653260/scipy-1.4.1.tar.gz (24.6MB)
-    100% |████████████████████████████████| 24.6MB 17kB/s 
-  Installing build dependencies ... done
-Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2)
-Collecting pandas (from morphocut)
-  Downloading https://www.piwheels.org/simple/pandas/pandas-0.25.3-cp37-cp37m-linux_armv7l.whl (33.1MB)
-    100% |████████████████████████████████| 33.1MB 12kB/s 
-Collecting PyWavelets>=0.4.0 (from scikit-image>=0.16.0->morphocut)
-  Downloading https://www.piwheels.org/simple/pywavelets/PyWavelets-1.1.1-cp37-cp37m-linux_armv7l.whl (6.1MB)
-    100% |████████████████████████████████| 6.1MB 67kB/s 
-Collecting networkx>=2.0 (from scikit-image>=0.16.0->morphocut)
-  Downloading https://files.pythonhosted.org/packages/41/8f/dd6a8e85946def36e4f2c69c84219af0fa5e832b018c970e92f2ad337e45/networkx-2.4-py3-none-any.whl (1.6MB)
-    100% |████████████████████████████████| 1.6MB 255kB/s 
-Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1)
-Collecting imageio>=2.3.0 (from scikit-image>=0.16.0->morphocut)
-  Downloading https://files.pythonhosted.org/packages/1a/de/f7f985018f462ceeffada7f6e609919fbcc934acd9301929cba14bc2c24a/imageio-2.6.1-py3-none-any.whl (3.3MB)
-    100% |████████████████████████████████| 3.3MB 123kB/s 
-Collecting python-dateutil>=2.6.1 (from pandas->morphocut)
-  Downloading https://files.pythonhosted.org/packages/d4/70/d60450c3dd48ef87586924207ae8907090de0b306af2bce5d134d78615cb/python_dateutil-2.8.1-py2.py3-none-any.whl (227kB)
-    100% |████████████████████████████████| 235kB 822kB/s 
-Collecting pytz>=2017.2 (from pandas->morphocut)
-  Downloading https://files.pythonhosted.org/packages/e7/f9/f0b53f88060247251bf481fa6ea62cd0d25bf1b11a87888e53ce5b7c8ad2/pytz-2019.3-py2.py3-none-any.whl (509kB)
-    100% |████████████████████████████████| 512kB 660kB/s 
-Collecting decorator>=4.3.0 (from networkx>=2.0->scikit-image>=0.16.0->morphocut)
-  Downloading https://files.pythonhosted.org/packages/8f/b7/f329cfdc75f3d28d12c65980e4469e2fa373f1953f5df6e370e84ea2e875/decorator-4.4.1-py2.py3-none-any.whl
-Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0)
-Building wheels for collected packages: scipy
-  Running setup.py bdist_wheel for scipy ... error
-  Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" bdist_wheel -d /tmp/pip-wheel-2w9xwni0 --python-tag cp37:
-  Traceback (most recent call last):
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
-      from . import multiarray
-  ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory
-  
-  During handling of the above exception, another exception occurred:
-  
-  Traceback (most recent call last):
-    File "<string>", line 1, in <module>
-    File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in <module>
-      setup_package()
-    File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package
-      from numpy.distutils.core import setup
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
-      from . import add_newdocs
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
-      from numpy.lib import add_newdoc
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
-      from .type_check import *
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
-      import numpy.core.numeric as _nx
-    File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
-      raise ImportError(msg)
-  ImportError:
-  Importing the multiarray numpy extension module failed.  Most
-  likely you are trying to import a failed build of numpy.
-  If you're working with a numpy git repo, try `git clean -xdf` (removes all
-  files not under version control).  Otherwise reinstall numpy.
-  
-  Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory
-  
-  
-  ----------------------------------------
-  Failed building wheel for scipy
-  Running setup.py clean for scipy
-  Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" clean --all:
-  
-  `setup.py clean` is not supported, use one of the following instead:
-  
-    - `git clean -xdf` (cleans all files)
-    - `git clean -Xdf` (cleans all versioned files, doesn't touch
-                        files that aren't checked into the git repo)
-  
-  Add `--force` to your command to use it anyway if you must (unsupported).
-  
-  
-  ----------------------------------------
-  Failed cleaning build dir for scipy
-Failed to build scipy
-Installing collected packages: PyWavelets, decorator, networkx, imageio, scikit-image, tqdm, scipy, python-dateutil, pytz, pandas, morphocut
-  Running setup.py install for scipy ... error
-    Complete output from command /usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-s4uxcq_l/install-record.txt --single-version-externally-managed --compile --user --prefix=:
-    
-    Note: if you need reliable uninstall behavior, then install
-    with pip instead of using `setup.py install`:
-    
-      - `pip install .`       (from a git repo or downloaded source
-                               release)
-      - `pip install scipy`   (last SciPy release on PyPI)
-    
-    
-    Traceback (most recent call last):
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 16, in <module>
-        from . import multiarray
-    ImportError: libf77blas.so.3: cannot open shared object file: No such file or directory
-    
-    During handling of the above exception, another exception occurred:
-    
-    Traceback (most recent call last):
-      File "<string>", line 1, in <module>
-      File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 540, in <module>
-        setup_package()
-      File "/tmp/pip-install-vrivsnzz/scipy/setup.py", line 516, in setup_package
-        from numpy.distutils.core import setup
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/__init__.py", line 142, in <module>
-        from . import add_newdocs
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
-        from numpy.lib import add_newdoc
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/__init__.py", line 8, in <module>
-        from .type_check import *
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/lib/type_check.py", line 11, in <module>
-        import numpy.core.numeric as _nx
-      File "/tmp/pip-build-env-3v411zsn/lib/python3.7/site-packages/numpy/core/__init__.py", line 26, in <module>
-        raise ImportError(msg)
-    ImportError:
-    Importing the multiarray numpy extension module failed.  Most
-    likely you are trying to import a failed build of numpy.
-    If you're working with a numpy git repo, try `git clean -xdf` (removes all
-    files not under version control).  Otherwise reinstall numpy.
-    
-    Original error was: libf77blas.so.3: cannot open shared object file: No such file or directory
-    
-    
-    ----------------------------------------
-Command "/usr/bin/python3 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-vrivsnzz/scipy/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-s4uxcq_l/install-record.txt --single-version-externally-managed --compile --user --prefix=" failed with error code 1 in /tmp/pip-install-vrivsnzz/scipy/
-#########################################################
-Installation of Scipy using sudo apt-get
-#########################################################
-
-$ sudo apt-get install python3-scipy
-Lecture des listes de paquets... Fait
-Construction de l'arbre des dépendances       
-Lecture des informations d'état... Fait
-Les paquets supplémentaires suivants seront installés : 
-  python3-decorator
-Paquets suggérés :
-  python-scipy-doc
-Les NOUVEAUX paquets suivants seront installés :
-  python3-decorator python3-scipy
-0 mis à jour, 2 nouvellement installés, 0 à enlever et 41 non mis à jour.
-Il est nécessaire de prendre 8 925 ko dans les archives.
-Après cette opération, 38,0 Mo d'espace disque supplémentaires seront utilisés.
-Souhaitez-vous continuer ? [O/n] o
-Réception de :1 http://ftp.igh.cnrs.fr/pub/os/linux/raspbian/raspbian buster/main armhf python3-decorator all 4.3.0-1.1 [14,5 kB]
-Réception de :2 http://ftp.igh.cnrs.fr/pub/os/linux/raspbian/raspbian buster/main armhf python3-scipy armhf 1.1.0-7 [8 910 kB]
-8 925 ko réceptionnés en 3s (2 561 ko/s)       
-Sélection du paquet python3-decorator précédemment désélectionné.
-(Lecture de la base de données... 99960 fichiers et répertoires déjà installés.)
-Préparation du dépaquetage de .../python3-decorator_4.3.0-1.1_all.deb ...
-Dépaquetage de python3-decorator (4.3.0-1.1) ...
-Sélection du paquet python3-scipy précédemment désélectionné.
-Préparation du dépaquetage de .../python3-scipy_1.1.0-7_armhf.deb ...
-Dépaquetage de python3-scipy (1.1.0-7) ...
-Paramétrage de python3-decorator (4.3.0-1.1) ...
-Paramétrage de python3-scipy (1.1.0-7) ...
-
-#########################################################
-Installation of MorphoCut packaged on PyPI via pip3 using sudo
-#########################################################
-
-$ sudo pip3 install morphocut
-Looking in indexes: https://pypi.org/simple, https://www.piwheels.org/simple
-Collecting morphocut
-  Using cached https://files.pythonhosted.org/packages/7e/c7/1addaf867234dd30db6d1f4bf8d3b685d93b743023a863814451abd5cef8/morphocut-0.1.1-py3-none-any.whl
-Requirement already satisfied: scikit-image>=0.16.0 in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.16.2)
-Requirement already satisfied: numpy in /usr/lib/python3/dist-packages (from morphocut) (1.16.2)
-Requirement already satisfied: tqdm in /usr/local/lib/python3.7/dist-packages (from morphocut) (4.41.1)
-Requirement already satisfied: pandas in /usr/local/lib/python3.7/dist-packages (from morphocut) (0.25.3)
-Requirement already satisfied: scipy in /usr/lib/python3/dist-packages (from morphocut) (1.1.0)
-Requirement already satisfied: imageio>=2.3.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (2.6.1)
-Requirement already satisfied: PyWavelets>=0.4.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (1.1.1)
-Requirement already satisfied: networkx>=2.0 in /usr/local/lib/python3.7/dist-packages (from scikit-image>=0.16.0->morphocut) (2.4)
-Requirement already satisfied: pillow>=4.3.0 in /usr/lib/python3/dist-packages (from scikit-image>=0.16.0->morphocut) (5.4.1)
-Requirement already satisfied: python-dateutil>=2.6.1 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2.8.1)
-Requirement already satisfied: pytz>=2017.2 in /usr/local/lib/python3.7/dist-packages (from pandas->morphocut) (2019.3)
-Requirement already satisfied: decorator>=4.3.0 in /usr/local/lib/python3.7/dist-packages (from networkx>=2.0->scikit-image>=0.16.0->morphocut) (4.4.1)
-Requirement already satisfied: six>=1.5 in /usr/lib/python3/dist-packages (from python-dateutil>=2.6.1->pandas->morphocut) (1.12.0)
-Installing collected packages: morphocut
-Successfully installed morphocut-0.1.1

morphocut/morphocut.py

@@ -1,169 +0,0 @@
-"""Experiment on processing KOSMOS data using MorphoCut."""
-
-import datetime
-import os
-
-from skimage.util import img_as_ubyte
-
-from morphocut import Call
-from morphocut.contrib.ecotaxa import EcotaxaWriter
-from morphocut.contrib.zooprocess import CalculateZooProcessFeatures
-from morphocut.core import Pipeline
-from morphocut.file import Find
-from morphocut.image import (
-    ExtractROI,
-    FindRegions,
-    ImageReader,
-    ImageWriter,
-    RescaleIntensity,
-    RGB2Gray,
-)
-from morphocut.stat import RunningMedian
-from morphocut.str import Format
-from morphocut.stream import TQDM, Enumerate
-
-from skimage.feature import canny
-from skimage.color import rgb2gray, label2rgb
-from skimage.morphology import disk
-from skimage.morphology import erosion, dilation, closing
-from skimage.measure import label, regionprops
-
-
-import_path = "/media/tpollina/rootfs/home/pi/Desktop/PlanktonScope_acquisition/01_17_2020/RAW"
-export_path = "/media/tpollina/rootfs/home/pi/Desktop/PlanktonScope_acquisition/01_17_2020/"
-CLEAN = os.path.join(export_path, "CLEAN")
-os.makedirs(CLEAN, exist_ok=True)
-
-
-OBJECTS = os.path.join(export_path, "OBJECTS")
-os.makedirs(OBJECTS, exist_ok=True)
-
-archive_fn = os.path.join(export_path, "ecotaxa_export.zip")
-
-# Meta data that is added to every object
-global_metadata = {
-    "acq_instrument": "Planktoscope",
-    "process_datetime": datetime.datetime.now(),
-    "sample_project": "PlanktonScope Villefranche",
-    "sample_ship": "Kayak de Fabien",
-    "sample_operator": "Thibaut Pollina",
-    "sample_id": "Flowcam_PlanktonScope_comparison",
-    "sample_sampling_gear": "net",
-    "sample_time":150000,
-    "sample_date":16112020,
-    "object_lat": 43.696146,
-    "object_lon": 7.308359,
-    "acq_fnumber_objective": 16,
-    "acq_celltype": 200,
-    "process_pixel": 1.19,
-    "acq_camera": "Pi Camera V2.1",
-    "acq_instrument": "PlanktonScope V2.1",
-    "acq_software": "Node-RED Dashboard and raw python",
-    "acq_instrument_ID": "copepode",
-    "acq_volume": 24,
-    "acq_flowrate": "Unknown",
-    "acq_camera.resolution" : "(3280, 2464)",
-    "acq_camera.iso" : 60,
-    "acq_camera.shutter_speed" : 100,
-    "acq_camera.exposure_mode" : 'off',
-    "acq_camera.awb_mode" : 'off',
-    "acq_nb_frames" : 1000
-}
-
-# Define processing pipeline
-with Pipeline() as p:
-    # Recursively find .jpg files in import_path.
-    # Sort to get consective frames.
-    abs_path = Find(import_path, [".jpg"], sort=True, verbose=True)
-
-    # Extract name from abs_path
-    name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
-
-    # Read image
-    img = ImageReader(abs_path)
-
-    # Apply running median to approximate the background image
-    flat_field = RunningMedian(img, 10)
-    
-    # Correct image
-    img = img / flat_field
-    
-    # Rescale intensities and convert to uint8 to speed up calculations
-    img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
-
-    # Convert image to uint8 gray
-    img_gray = RGB2Gray(img)
-
-    img_gray = Call(img_as_ubyte, img_gray)
-
-    img_canny = Call(canny, img_gray, sigma=0.3)
-
-    img_dilate = Call(dilation, img_canny)
-
-    img_closing = Call(closing, img_dilate)
-
-    mask = Call(erosion, img_closing)
-
-    # Show progress bar for frames
-    TQDM(Format("Frame {name}", name=name))
-    
-    # Apply threshold find objects
-    #threshold = 204  # Call(skimage.filters.threshold_otsu, img_gray)
-    #mask = img_gray < threshold
-
-    # Write corrected frames
-    frame_fn = Format(os.path.join(CLEAN, "{name}.jpg"), name=name)
-    ImageWriter(frame_fn, img)
-
-    # Find objects
-    regionprops = FindRegions(
-        mask, img_gray, min_area=1000, padding=10, warn_empty=name
-    )
-
-    # For an object, extract a vignette/ROI from the image
-    roi_orig = ExtractROI(img, regionprops, bg_color=255)
-
-    roi_orig
-    # Generate an object identifier
-    i = Enumerate()
-    #Call(print,i)
-
-    object_id = Format("{name}_{i:d}", name=name, i=i)
-    #Call(print,object_id)
-    
-    object_fn = Format(os.path.join(OBJECTS, "{name}.jpg"), name=object_id)
-    ImageWriter(object_fn, roi_orig)
-
-
-    # Calculate features. The calculated features are added to the global_metadata.
-    # Returns a Variable representing a dict for every object in the stream.
-    meta = CalculateZooProcessFeatures(
-        regionprops, prefix="object_", meta=global_metadata
-    )
-    # If CalculateZooProcessFeatures is not used, we need to copy global_metadata into the stream:
-    # meta = Call(lambda: global_metadata.copy())
-    # https://github.com/morphocut/morphocut/issues/51
-
-    # Add object_id to the metadata dictionary
-    meta["object_id"] = object_id
-
-    # Generate object filenames
-    orig_fn = Format("{object_id}.jpg", object_id=object_id)
-
-    # Write objects to an EcoTaxa archive:
-    # roi image in original color, roi image in grayscale, metadata associated with each object
-    EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)
-
-    # Progress bar for objects
-    TQDM(Format("Object {object_id}", object_id=object_id))
-
-
-import datetime
-
-BEGIN = datetime.datetime.now()
-# Execute pipeline
-p.run() 
-
-END = datetime.datetime.now()
-
-print("MORPHOCUT    :"+str(END-BEGIN))

morphocut/morphocut_opencv.py

@@ -1,181 +0,0 @@
-"""Experiment on processing KOSMOS data using MorphoCut."""
-
-import datetime
-import os
-
-from skimage.util import img_as_ubyte
-
-from morphocut import Call
-from morphocut.contrib.ecotaxa import EcotaxaWriter
-from morphocut.contrib.zooprocess import CalculateZooProcessFeatures
-from morphocut.core import Pipeline
-from morphocut.file import Find
-from morphocut.image import (
-    ExtractROI,
-    FindRegions,
-    ImageReader,
-    ImageWriter,
-    RescaleIntensity,
-    RGB2Gray,
-)
-from morphocut.stat import RunningMedian
-from morphocut.str import Format
-from morphocut.stream import TQDM, Enumerate, FilterVariables
-
-from skimage.feature import canny
-from skimage.color import rgb2gray, label2rgb
-from skimage.morphology import disk
-from skimage.morphology import erosion, dilation, closing
-from skimage.measure import label, regionprops
-import cv2
-
-import_path = "/home/tpollina/Desktop/JUPYTER/IMAGES/RAW"
-export_path = "/home/tpollina/Desktop/JUPYTER/IMAGES/"
-
-CLEAN = os.path.join(export_path, "CLEAN")
-os.makedirs(CLEAN, exist_ok=True)
-
-
-ANNOTATED = os.path.join(export_path, "ANNOTATED")
-os.makedirs(ANNOTATED, exist_ok=True)
-
-
-OBJECTS = os.path.join(export_path, "OBJECTS")
-os.makedirs(OBJECTS, exist_ok=True)
-
-archive_fn = os.path.join(export_path, "ecotaxa_export.zip")
-
-# Meta data that is added to every object
-global_metadata = {
-    "acq_instrument": "Planktoscope",
-    "process_datetime": datetime.datetime.now(),
-    "sample_project": "PlanktonScope Villefranche",
-    "sample_ship": "Kayak de Fabien",
-    "sample_operator": "Thibaut Pollina",
-    "sample_id": "Flowcam_PlanktonScope_comparison",
-    "sample_sampling_gear": "net",
-    "sample_time":150000,
-    "sample_date":16112020,
-    "object_lat": 43.696146,
-    "object_lon": 7.308359,
-    "acq_fnumber_objective": 16,
-    "acq_celltype": 200,
-    "process_pixel": 1.19,
-    "acq_camera": "Pi Camera V2.1",
-    "acq_instrument": "PlanktonScope V2.1",
-    "acq_software": "Node-RED Dashboard and raw python",
-    "acq_instrument_ID": "copepode",
-    "acq_volume": 24,
-    "acq_flowrate": "Unknown",
-    "acq_camera.resolution" : "(3280, 2464)",
-    "acq_camera.iso" : 60,
-    "acq_camera.shutter_speed" : 100,
-    "acq_camera.exposure_mode" : 'off',
-    "acq_camera.awb_mode" : 'off',
-    "acq_nb_frames" : 1000
-}
-
-# Define processing pipeline
-with Pipeline() as p:
-    # Recursively find .jpg files in import_path.
-    # Sort to get consective frames.
-    abs_path = Find(import_path, [".jpg"], sort=True, verbose=True)
-
-    # Extract name from abs_path
-    name = Call(lambda p: os.path.splitext(os.path.basename(p))[0], abs_path)
-
-    # Read image
-    img = ImageReader(abs_path)
-
-    # Show progress bar for frames
-    #TQDM(Format("Frame {name}", name=name))
-    
-    # Apply running median to approximate the background image
-    flat_field = RunningMedian(img, 5)
-
-    # Correct image
-    img = img / flat_field
-    
-    # Rescale intensities and convert to uint8 to speed up calculations
-    img = RescaleIntensity(img, in_range=(0, 1.1), dtype="uint8")
-    
-    FilterVariables(name,img)
-    #
-    frame_fn = Format(os.path.join(CLEAN, "{name}.jpg"), name=name)
-    ImageWriter(frame_fn, img)
-    
-    # Convert image to uint8 gray
-    img_gray = RGB2Gray(img)
-    
-    # ?
-    img_gray = Call(img_as_ubyte, img_gray)
-
-    #Canny edge detection
-    img_canny = Call(cv2.Canny, img_gray, 50,100)
-
-    #Dilate
-    kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
-    img_dilate = Call(cv2.dilate, img_canny, kernel, iterations=2)
-    
-    #Close
-    kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (5, 5))
-    img_close = Call(cv2.morphologyEx, img_dilate, cv2.MORPH_CLOSE, kernel, iterations=1)
-     
-    #Erode
-    kernel = Call(cv2.getStructuringElement, cv2.MORPH_ELLIPSE, (15, 15))
-    mask = Call(cv2.erode, img_close, kernel, iterations=2)
-    
-    frame_fn = Format(os.path.join(ANNOTATED, "{name}.jpg"), name=name)
-    ImageWriter(frame_fn, mask)
-    
-    # Find objects
-    regionprops = FindRegions(
-        mask, img_gray, min_area=1000, padding=10, warn_empty=name
-    )
-    # For an object, extract a vignette/ROI from the image
-    roi_orig = ExtractROI(img, regionprops, bg_color=255)
-    
-    # For an object, extract a vignette/ROI from the image
-    roi_mask = ExtractROI(mask, regionprops, bg_color=255)
-
-
-    # Generate an object identifier
-    i = Enumerate()
-    #Call(print,i)
-
-    object_id = Format("{name}_{i:d}", name=name, i=i)
-    #Call(print,object_id)
-    
-    object_fn = Format(os.path.join(OBJECTS, "{name}.jpg"), name=object_id)
-    ImageWriter(object_fn, roi_orig)
-
-
-    # Calculate features. The calculated features are added to the global_metadata.
-    # Returns a Variable representing a dict for every object in the stream.
-    meta = CalculateZooProcessFeatures(
-        regionprops, prefix="object_", meta=global_metadata
-    )
-    
-    # Add object_id to the metadata dictionary
-    meta["object_id"] = object_id
-
-    # Generate object filenames
-    orig_fn = Format("{object_id}.jpg", object_id=object_id)
-
-    # Write objects to an EcoTaxa archive:
-    # roi image in original color, roi image in grayscale, metadata associated with each object
-    EcotaxaWriter(archive_fn, (orig_fn, roi_orig), meta)
-
-    # Progress bar for objects
-    TQDM(Format("Object {object_id}", object_id=object_id))
-
-
-import datetime
-
-BEGIN = datetime.datetime.now()
-# Execute pipeline
-p.run() 
-
-END = datetime.datetime.now()
-
-print("MORPHOCUT    :"+str(END-BEGIN))

scripts/gallery/gallery.conf

@@ -15,12 +15,12 @@ server {
         }
 
         location @autoindex {
-                xslt_stylesheet /home/pi/PlanktonScope/scripts/gallery/nginx_template.xslt path='$uri';
+                xslt_stylesheet /home/pi/PlanktoScope/scripts/gallery/nginx_template.xslt path='$uri';
         }
 
         # assets, media
         location ~* \.(?:css(\.map)?|js(\.map)?|svg|ttf|eot|woff|woff2)$ {
-                root /home/pi/PlanktonScope/scripts/gallery/;
+                root /home/pi/PlanktoScope/scripts/gallery/;
                 expires    30d;
                 access_log off;
         }

scripts/main.py

@@ -41,22 +41,22 @@ logger.info("Starting the PlanktoScope python script!")
 # Library for exchaning messages with Node-RED
 import planktoscope.mqtt
 
-# Import the planktonscope stepper module
+# Import the planktoscope stepper module
 import planktoscope.stepper
 
-# Import the planktonscope imager module
+# Import the planktoscope imager module
 import planktoscope.imager
 
-# Import the planktonscope segmenter module
+# Import the planktoscope segmenter module
 import planktoscope.segmenter
 
-# Import the planktonscope LED module
+# Import the planktoscope LED module
 import planktoscope.light
 
-# Import the planktonscope uuidName module
+# Import the planktoscope uuidName module
 import planktoscope.uuidName
 
-# Import the planktonscope display module for the OLED screen
+# Import the planktoscope display module for the OLED screen
 import planktoscope.display
 
 # global variable that keeps the wheels spinning
@@ -93,13 +93,13 @@ if __name__ == "__main__":
                 sys.exit(1)
 
     # Let's make sure the used base path exists
-    img_path = "/home/pi/PlanktonScope/img"
+    img_path = "/home/pi/PlanktoScope/img"
     # check if this path exists
     if not os.path.exists(img_path):
         # create the path!
         os.makedirs(img_path)
 
-    export_path = "/home/pi/PlanktonScope/export"
+    export_path = "/home/pi/PlanktoScope/export"
     # check if this path exists
     if not os.path.exists(export_path):
         # create the path!

scripts/planktoscope/imager/__init__.py

@@ -66,9 +66,9 @@ class ImagerProcess(multiprocessing.Process):
 
         logger.info("planktoscope.imager is initialising")
 
-        if os.path.exists("/home/pi/PlanktonScope/hardware.json"):
+        if os.path.exists("/home/pi/PlanktoScope/hardware.json"):
             # load hardware.json
-            with open("/home/pi/PlanktonScope/hardware.json", "r") as config_file:
+            with open("/home/pi/PlanktoScope/hardware.json", "r") as config_file:
                 configuration = json.load(config_file)
                 logger.debug(f"Hardware configuration loaded is {configuration}")
         else:

scripts/planktoscope/imager/raspimjpeg.py

@@ -21,8 +21,8 @@ import subprocess  # nosec
 ################################################################################
 class raspimjpeg(object):
     def __init__(self, *args, **kwargs):
-        self.__configfile = "/home/pi/PlanktonScope/scripts/raspimjpeg/raspimjpeg.conf"
+        self.__configfile = "/home/pi/PlanktoScope/scripts/raspimjpeg/raspimjpeg.conf"
-        self.__binary = "/home/pi/PlanktonScope/scripts/raspimjpeg/bin/raspimjpeg"
+        self.__binary = "/home/pi/PlanktoScope/scripts/raspimjpeg/bin/raspimjpeg"
         self.__statusfile = "/dev/shm/mjpeg/status_mjpeg.txt"  # nosec
         self.__pipe = "/dev/shm/mjpeg/FIFO"  # nosec
         self.__sensor_name = ""

scripts/planktoscope/segmenter/__init__.py

@@ -975,9 +975,4 @@ class SegmenterProcess(multiprocessing.Process):
 # This is called if this script is launched directly
 if __name__ == "__main__":
     # TODO This should be a test suite for this library
-    segmenter_thread = SegmenterProcess(
+    pass
-        None, "/home/rbazile/Documents/pro/PlanktonPlanet/Planktonscope/Segmenter/data/"
-    )
-    segmenter_thread.segment_path(
-        "/home/rbazile/Documents/pro/PlanktonPlanet/Planktonscope/Segmenter/data/test"
-    )

scripts/planktoscope/segmenter/ecotaxa.py

@@ -18,7 +18,7 @@ Example of metadata file received
   "sample_sampling_gear": "net_hsn",
   "sample_concentrated_sample_volume": 100,
   "acq_id": "Tara atlantique sud 2021_hsn_2021_01_22_1",
-  "acq_instrument": "PlanktonScope v2.2",
+  "acq_instrument": "PlanktoScope v2.2",
   "acq_instrument_id": "Babane Batoukoa",
   "acq_celltype": 300,
   "acq_minimum_mesh": 20,

scripts/planktoscope/stepper.py

@@ -165,10 +165,10 @@ class stepper:
 class StepperProcess(multiprocessing.Process):
 
     focus_steps_per_mm = 40
-    # 507 steps per ml for Planktonscope standard
+    # 507 steps per ml for PlanktoScope standard
     # 5200 for custom NEMA14 pump with 0.8mm ID Tube
     pump_steps_per_ml = 507
-    # focus max speed is in mm/sec and is limited by the maximum number of pulses per second the Planktonscope can send
+    # focus max speed is in mm/sec and is limited by the maximum number of pulses per second the PlanktoScope can send
     focus_max_speed = 0.5
     # pump max speed is in ml/min
     pump_max_speed = 30
@@ -182,9 +182,9 @@ class StepperProcess(multiprocessing.Process):
 
         self.stop_event = event
 
-        if os.path.exists("/home/pi/PlanktonScope/hardware.json"):
+        if os.path.exists("/home/pi/PlanktoScope/hardware.json"):
             # load hardware.json
-            with open("/home/pi/PlanktonScope/hardware.json", "r") as config_file:
+            with open("/home/pi/PlanktoScope/hardware.json", "r") as config_file:
                 configuration = json.load(config_file)
                 logger.debug(f"Hardware configuration loaded is {configuration}")
         else:

scripts/raspimjpeg/raspimjpeg.conf

@@ -118,7 +118,7 @@ motion_file 0
 # macros_path can be used to store macros executed by sy command
 # boxing_path if set is where h264 files will be temporarily stored when boxing used
 # image, video and lapse may be configured relative to media_path if first / left out
-base_path /home/pi/PlanktonScope/scripts/raspimjpeg/
+base_path /home/pi/PlanktoScope/scripts/raspimjpeg/
 preview_path /dev/shm/mjpeg/cam.jpg
 image_path /dev/shm/mjpeg/image.jpg
 lapse_path /dev/shm/mjpeg/tl_%i_%t_%Y%M%D_%h%m%s.jpg
@@ -126,7 +126,7 @@ video_path /dev/shm/mjpeg/vi_%v_%Y%M%D_%h%m%s.mp4
 status_file /dev/shm/mjpeg/status_mjpeg.txt
 control_file /dev/shm/mjpeg/FIFO
 media_path /home/pi/data/
-macros_path /home/pi/PlanktonScope/scripts/raspimjpeg/macros
+macros_path /home/pi/PlanktoScope/scripts/raspimjpeg/macros
 user_annotate /dev/shm/mjpeg/user_annotate.txt
 boxing_path
 subdir_char @
@@ -168,9 +168,9 @@ callback_timeout 30
 user_config
 
 #logfile for raspimjpeg, default to merge with scheduler log
-log_file /home/pi/PlanktonScope/scripts/raspimjpeg/raspimjpeg.log
+log_file /home/pi/PlanktoScope/scripts/raspimjpeg/raspimjpeg.log
 log_size 10000
-motion_logfile /home/pi/PlanktonScope/scripts/raspimjpeg/motion.log
+motion_logfile /home/pi/PlanktoScope/scripts/raspimjpeg/motion.log
 
 #enforce_lf set to 1 to only process FIFO commands when terminated with LF
 enforce_lf 1