Merge pull request #57 from Gregor-Mendel-Institute/1.3

Merge 1.3 > master

.github/workflows/docker_base.yml

@@ -1,4 +1,4 @@
-name: Docker Container (Base)
+name: Container build (Base)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-base
-          path: containers/base
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-base
-          path: containers/base
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-base containers/base
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-base docker://quay.io/beckerlab/aradeepopsis-base:${GITHUB_REF##*/}

.github/workflows/docker_dpp.yml

@@ -1,4 +1,4 @@
-name: Docker Container (DPP)
+name: Container build (DPP)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-dpp
-          path: containers/addons/dpp
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-dpp
-          path: containers/addons/dpp
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-dpp containers/addons/dpp
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-dpp docker://quay.io/beckerlab/aradeepopsis-dpp:${GITHUB_REF##*/}

.github/workflows/docker_shiny.yml

@@ -1,4 +1,4 @@
-name: Docker Container (Shiny)
+name: Container build (Shiny)
 
 on:
   push:
@@ -8,25 +8,20 @@ on:
 
 jobs:
   push_to_registry:
-    name: Push Docker image to GitHub Packages
+    name: Push to quay.io
     runs-on: ubuntu-latest
     steps:
       - name: Check out the repo
         uses: actions/checkout@v2
-      - name: Push to Docker Hub
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ secrets.DOCKER_USER }}
-          password: ${{ secrets.DOCKER_PASSWORD }}
-          repository: beckerlab/aradeepopsis-shiny
-          path: containers/shiny
-          tag_with_ref: true
-      - name: Push to GitHub Packages
-        uses: docker/build-push-action@v1
-        with:
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-          registry: docker.pkg.github.com
-          repository: gregor-mendel-institute/aradeepopsis/aradeepopsis-shiny
-          path: containers/shiny
-          tag_with_ref: true
+
+      - name: Login to quay.io
+        env:
+          QUAY_USER: ${{ secrets.REGISTRY_USER }}
+          QUAY_PASSWORD: ${{ secrets.REGISTRY_PASSWORD }}
+        run: podman login -u ${QUAY_USER} -p ${QUAY_PASSWORD} quay.io
+
+      - name: Build container
+        run: podman build --tag beckerlab/aradeepopsis-shiny containers/shiny
+
+      - name: Push container
+        run: podman push beckerlab/aradeepopsis-shiny docker://quay.io/beckerlab/aradeepopsis-shiny:${GITHUB_REF##*/}

.github/workflows/minimal_test.yml

@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        nxf_ver: ["20.01.0", ""]
+        nxf_ver: ["20.07.1", ""]
     steps:
       - uses: actions/checkout@v2
 

CHANGELOG.md

@@ -1,5 +1,19 @@
 # Changelog
 
+## [v1.3](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.3) - 2021-01-11
+
+* changed container registry from docker.io to quay.io
+* improved image visualization and plot rendering in Shiny app (see [#54](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/54)) thanks @dschneiderch for input
+* updated `scikit-image` `0.17.2` > `0.18.1`
+* updated `imagemagick` dependency `7.0.10_23` > `7.0.10_28`
+* updated `shinycssloaders` dependency `0.3` > `1.0.0`
+* updated `slickr` dependency `0.4.9` > `0.5.0`
+* added publication doi to pipeline manifest
+* changed (back) download links in pipeline to fetch pretrained models from Dropbox instead of Zenodo ([#53](https://github.com/Gregor-Mendel-Institute/aradeepopsis/issues/53#issue-779431868))
+* added charliecloud profile (needs nextflow >= 20.12.0-edge)
+* fixed plotting of leaf states over time in Shiny app (when appropriate metadata are provided)
+* added config for LRZ coolmuc2
+
 ## [v1.2.1](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.2.1) - 2020-07-23
 
 * updated pipeline to fetch trained models from the deposited [Zenodo record](https://doi.org/10.5281/zenodo.3946321) instead of Dropbox
@@ -30,4 +44,4 @@
 
 ## [v1.0](https://github.com/Gregor-Mendel-Institute/aradeepopsis/releases/tag/v1.0) - 2020-04-02
 
-Initial pipeline release
+Initial pipeline release

README.md

@@ -4,16 +4,9 @@
 ![Latest Release](https://img.shields.io/github/v/release/Gregor-Mendel-Institute/aradeepopsis?sort=semver)
 ![License](https://img.shields.io/github/license/Gregor-Mendel-Institute/aradeepopsis)
 [![DOI](https://zenodo.org/badge/240287274.svg)](https://zenodo.org/badge/latestdoi/240287274)
-[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.01.0-important.svg)](https://www.nextflow.io/)
+[![Nextflow](https://img.shields.io/badge/nextflow-%E2%89%A520.07.1-important.svg)](https://www.nextflow.io/)
 [![conda](https://img.shields.io/badge/install%20with-conda-brightgreen.svg)](https://conda.io/)
 
-| Container  | Image size  | Pulls | Latest version  | 
-| :---: | :---: | :---: | :---: |
-| ![Docker Container (Base)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Base)/badge.svg?branch=master) | ![Docker Size (Base)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-base?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-base) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) |
-| ![Docker Container (Shiny)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(Shiny)/badge.svg?branch=master)  | ![Docker Size (Shiny)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-shiny?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-shiny) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-shiny?sort=semver) |
-| ![Docker Docker (DPP)](https://github.com/Gregor-Mendel-Institute/aradeepopsis/workflows/Docker%20Container%20(DPP)/badge.svg?branch=master) | ![Docker Size (DPP)](https://img.shields.io/docker/image-size/beckerlab/aradeepopsis-dpp?sort=semver) | ![Pulls](https://img.shields.io/docker/pulls/beckerlab/aradeepopsis-dpp) | ![Image Tag](https://img.shields.io/docker/v/beckerlab/aradeepopsis-base?sort=semver) |
-
-
 # Introduction
 
 `ARADEEPOPSIS` is a software tool that enables plant researchers to non-invasively score plant growth, biomass accumulation and senescence from image data in a highly parallelized, high throughput, yet easy to use manner.

assets/shiny/app.R

@@ -1,18 +1,18 @@
-# Copyright (C) 2019-2020 Patrick Hüther
+# Copyright (C) 2019-2021 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 
 library(shiny)
 library(slickR)
@@ -42,10 +42,10 @@ traitcount <- ncol(data) - 2 # exclude filename and suffix
 imagecount <- nrow(data)
 
 # Define UI
-ui <- navbarPage(title="aradeepopsis", id="nav", theme = shinytheme("flatly"),
+ui <- navbarPage(title=a("aradeepopsis", href="https://github.com/Gregor-Mendel-Institute/aradeepopsis", target="_blank"), windowTitle = "ARADEEPOPSIS", id="nav", theme = shinytheme("flatly"), collapsible=TRUE,
 		tabPanel("Rosette Carousel",
 			sliderInput("chunk", label = "Select chunk:", min = 1, max = ceiling(imagecount/60), value = 1, width = '100%', step = 1),
-			slickROutput("slickr",width='100%',height='400px') %>% withSpinner()
+			slickROutput("slickr", width='auto', height='auto') %>% withSpinner()
 		),
 		tabPanel("Rosette Explorer",
 			sidebarPanel(
@@ -92,7 +92,7 @@ ui <- navbarPage(title="aradeepopsis", id="nav", theme = shinytheme("flatly"),
 				div(style = "overflow-x:scroll;", tableOutput("meta")),
 				varSelectizeInput("file","Select column containing the filename", data = NULL),
 				varSelectizeInput("date","Select column containing the timestamp", data = NULL),
-				textInput("date_format","Enter timestamp format",value="%y-%m-%d"),
+				textInput("date_format",HTML('Enter timestamp <a href="https://rdrr.io/r/base/strptime.html">format</a>'),value="%y-%m-%d"),
 				varSelectizeInput("groupvar","Select column to group by", data = NULL),
 				actionButton("merge_data", "Analyze!"),
 				conditionalPanel(
@@ -129,18 +129,18 @@ server <- function(input, output, session) {
 		updateSelectizeInput(session, "explorer_files", choices = c(imagenames), server = TRUE)
 
 		output$mask <- renderImage(deleteFile=FALSE,{
-			list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=400,height=400)
+			list(src = glue::glue("diagnostics/mask/mask_{input$explorer_files}.png"),width=600,height="auto")
 		})
 		output$hull <- renderImage(deleteFile=FALSE,{
-			list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=400,height=400)
+			list(src = glue::glue("diagnostics/convex_hull/hull_{input$explorer_files}.png"),width=600,height="auto")
 		})
 		output$rosette <- renderImage(deleteFile=FALSE,{
-			list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=400,height=400)
+			list(src = glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"),width=600,height="auto")
 		})
 		output$overlay <- renderImage(deleteFile=FALSE,{
-			list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=400,height=400)
+			list(src = glue::glue("diagnostics/overlay/overlay_{input$explorer_files}.jpeg"),width=600,height="auto")
 		})
-		output$color <- renderPlot({
+		output$color <- renderPlot(width=600,height=600,{
 	    img <- readJPEG(glue::glue("diagnostics/crop/crop_{input$explorer_files}.jpeg"))
 
 	    r <- img[,,1] %>% as_tibble() %>% pivot_longer(everything()) %>% mutate(name=1)
@@ -214,26 +214,27 @@ server <- function(input, output, session) {
 			joined() %>%
 		    select(dateVar,groupVar,trait := !!input$exp_traits) %>%
 		    ggplot(aes(x=dateVar,y=trait,colour=groupVar)) +
-		    stat_summary(geom="line") +
+		    stat_summary(geom="line", size=1.5) +
 		    stat_summary(geom="pointrange") +
-				scale_color_viridis_d(option="A") +
+				scale_color_viridis_d(option="A", end=0.9) +
 		    labs(x="time",y="trait value",colour=element_blank()) +
 				theme_bw()
 		})
 		output$leafstates <- renderPlot({
 		  joined() %>%
-		    select(file_name,groupVar,dateVar,matches("norm_area|antho_area|senesc_area")) %>%
+		    select(file,groupVar,dateVar,matches("norm_area|antho_area|senesc_area")) %>%
 		    pivot_longer(starts_with("class_"),names_to = "state") %>%
-		    group_by(groupVar,dateVar,file_name) %>%
+		    group_by(groupVar,dateVar,file) %>%
 		    mutate(relativeFrac=value/sum(value)) %>%
 		    ggplot(aes(x = dateVar, y = relativeFrac, colour=state)) +
-		    stat_summary(geom="line") +
+		    stat_summary(geom="line", size=1.5) +
 		    stat_summary(geom="pointrange") +
 		    scale_color_manual(values = c("class_norm_area" = rgb(31,158,137, maxColorValue = 255),
 		                                  "class_antho_area" = rgb(72,40,120, maxColorValue = 255),
 		                                  "class_senesc_area" =  rgb(253,231,37, maxColorValue = 255))) +
 		    scale_y_continuous(labels = scales::percent) +
 		    labs(x="time",y="% of plant area",colour=element_blank()) +
+			facet_wrap(~groupVar) +
 		    theme_bw()
 		})
 		# show a description if Rosette Experiment is selected
@@ -243,12 +244,14 @@ server <- function(input, output, session) {
 					modalDialog(
 						title="Experimental feature!",
 						HTML("This feature is meant to add metadata to the pipeline result, allowing to visualize traits over time.<br>
-						It requires a table with metadata in csv format.<br>
-						Such metadata has to contain one row per input image and columns with the following information:<br>
-						- filename of the original image<br>
-						- timestamp when the image was recorded<br>
-						- <a href='https://rdrr.io/r/base/strptime.html'>format</a> of the timestamp<br>
-						- variable by which the result should be grouped (such as a genotype ID)")
+						It requires a csv table with metadata that is then joined with the pipeline result.<br>
+						<br>
+						Such metadata has to contain one row per input image and the following columns:<br>
+						- Filenames of the original images <br>
+						- Timestamps when the images were recorded<br>
+						- Variable(s) by which the result should be grouped (such as genotype or accession ID)<br>
+						<br>
+						Note: If the 'file' column of aradeepopsis_traits.csv is used to extract such metadata, trait columns should be removed before uploading")
 					)
 				)
 			}
@@ -262,7 +265,7 @@ server <- function(input, output, session) {
 			# this drastically improves page loading time
 			chunks <- if (imagecount > 60) split(imagenames$file, ceiling(seq_along(imagenames$file)/60)) else split(imagenames$file, 1)
 
-			opts <- settings(slidesToShow = 6, slidesToScroll = 6)
+			opts <- settings(slidesToShow=6, slidesToScroll=6, responsive=htmlwidgets::JS("[{breakpoint: 1440,settings: {slidesToShow: 3,slidesToScroll: 3}},{breakpoint: 680,settings: {slidesToShow: 1,slidesToScroll: 1}}]"))
 
 			overlay <- slickR(glue::glue("diagnostics/overlay/overlay_{chunks[[input$chunk]]}.jpeg"), height = 200) + opts
 			mask <- slickR(glue::glue("diagnostics/mask/mask_{chunks[[input$chunk]]}.png"), height = 200) + opts + settings(arrows = F)

bin/data_record.py

@@ -2,19 +2,19 @@
 
 # Copyright (C) 2019-2020 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 
 import tensorflow as tf
 

bin/frozen_graph.py

@@ -2,19 +2,19 @@
 
 # Copyright (C) 2019-2020 Patrick Hüther
 #
-# This file is part of araDeepopsis.
-# araDeepopsis free software: you can redistribute it and/or modify
+# This file is part of ARADEEPOPSIS.
+# ARADEEPOPSIS is free software: you can redistribute it and/or modify
 # it under the terms of the GNU General Public License as published by
 # the Free Software Foundation, either version 3 of the License, or
 # (at your option) any later version.
 #
-# araDeepopsis is distributed in the hope that it will be useful,
+# ARADEEPOPSIS is distributed in the hope that it will be useful,
 # but WITHOUT ANY WARRANTY; without even the implied warranty of
 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 # GNU General Public License for more details.
 #
 # You should have received a copy of the GNU General Public License
-# along with araDeepopsis.  If not, see <https://www.gnu.org/licenses/>.
+# along with ARADEEPOPSIS.  If not, see <https://www.gnu.org/licenses/>.
 # ======================================================================
 # Portions of this code are modifications based on work created and
 # shared by Google and used according to terms described in the