diff --git a/NAERSTADMO.cfg b/NAERSTADMO.cfg
index 35d768378a42c3a88692c5e53bc5621f818f87ae..d255f4a5ef1a98b0f73e2d956e7003375e9725aa 100644
--- a/NAERSTADMO.cfg
+++ b/NAERSTADMO.cfg
@@ -4,12 +4,14 @@ languages=en,nb
[i18n.en]
no_forecast = No forecast
-no_risk = No risk
-possible_risk = Possible risk
-high_risk = High risk
+no_risk = No infection risk
+possible_risk = Possible infection risk
+high_risk = High infection risk
+risk = Infection risk
[i18n.nb]
no_forecast = Varsel beregnes ikke
-no_risk = Ingen infeksjonsrisiko
+no_risk = Ingen fare for angrep
possible_risk = Mulig fare for angrep
-high_risk = Høy fare for angrep
+high_risk = Stor fare for angrep
+risk = Infeksjonsrisiko
diff --git a/NAERSTADMO.py b/NAERSTADMO.py
index 5bf37c8e37adefb9636b74abb0f361f2b1208750..e29026a4c948959fd449bba8415228b9d3e79fff 100644
--- a/NAERSTADMO.py
+++ b/NAERSTADMO.py
@@ -1,8 +1,26 @@
#!/usr/bin/python3
+"""
+ Copyright (C) 2023 NIBIO <https://www.nibio.no/>.
+
+ This program is free software: you can redistribute it and/or modify
+ it under the terms of the GNU Affero General Public License as
+ published by the Free Software Foundation, either version 3 of the
+ License, or (at your option) any later version.
+
+ This program 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 Affero General Public License for more details.
+
+ You should have received a copy of the GNU Affero General Public License
+ along with this program. If not, see <https://www.gnu.org/licenses/>.
+"""
+
+# Author: Brita Linnestad <brita.linnestad@nibio.no>
+
import os
-import subprocess
-import glob
+import subprocess,glob
from dotenv import load_dotenv
from datetime import datetime, timedelta
from jinja2 import Environment, FileSystemLoader
diff --git a/README.md b/README.md
index 0af07e81b03d9bc9be07ba7c7af11a104a321fe5..c7d2f2c620e3d9c3b420a2cece40e38838fbb19e 100644
--- a/README.md
+++ b/README.md
@@ -1,23 +1,70 @@
-# Naerstad Poteto Blight - spatial version
-
+# Naerstad Potato Blight Model - spatial version
+The model is based on several years of experiments where trap plants have been placed next to a potato field infected with late blight. Infections on these plants have been correlated with weather conditions the day of exposure, and this is the data the model is based on. The model predicts if there are favorable conditions for spore production and the following spread, survival and infection of these spores. The model produces an infection risk, and a value of 2.5 corresponds to one spot of late blight on each trap plant exposed. This value of 2.5 is the threshold where the model issues a warning.
## Technical description
-
-
-###Software requirements
+### Software requirements
The model can only be run on Linux, as some of the tools mentioned below are only available on Linux. The development and testing of the model has been done using Ubuntu Linux 22.04LTS.
-####CDO and GDAL
+#### CDO and GDAL
The heavy lifting in this model is done by the tools CDO and GDAL. These tools need to be installed and available. CDO is only available on Linux.
-####Python requirements
-The Python requirements are specified in requirements.txt file, and are included in the virtualenv created by the run_NAERSTADMO.sh (see below).
+#### Python requirements
+The Python requirements are specified in the `requirements.txt` file, and are included in the virtualenv created by the `run_NAERSTADMO.sh` (see below).
+
+#### Input data requirements
+The model assumes weather data files named `met_1_0km_nordic-[YYYY-MM-DD].nc` with hourly values of:
+* Temperature (TM)
+* Relative humidity (UM)
+* Precipitation (RR)
+* Wind speed (FF)
+* Global radiation (Q0)
+
+#### Running the model
+It is required that you have set the following environment variables:
+
+```bash
+# Path to this code (HOME_DIR + NAERSTADMO)
+HOME_DIR=/foobar/gridmodels/
+# Path to the weather data files. Expecting hourly values in files named met_1_0km_nordic-[YYYY-MM-DD].nc
+WEATHER_DATA_DIR=/foobar/met_1_0km_nordic/2024/
+# Start date for the model
+START_DATE=2024-05-15
+# Use this file to crop the output of the grid
+MASK_FILE=Norge_landomrader.csv
+# Where the GeoTIFF files will be output
+DATA_DIR=/foobar/mapserver/data/NAERSTADMO/
+# Where the mapfile will be output
+MAPFILE_DIR=/foobar/mapserver/wms/NAERSTADMO/
+# Path to the GeoTIFF files used by mapserver (written to mapfile)
+MAPSERVER_DATA_DIR=/foobar2/mapserver/data/NAERSTADMO/
+# Path to the mapfile used by mapserver (written to mapfile)
+MAPSERVER_MAPFILE_DIR=/foobar2/mapserver/wms/NAERSTADMO/
+# Path to the mapserver log file for this WMS (written to mapfile)
+MAPSERVER_LOG_FILE=/foobar2/mapserver/log/NAERSTADMO.log
+# Path for mapserver to store tmp images (written to mapfile)
+MAPSERVER_IMAGE_PATH=/foobar2/mapserver/tmp/
+# Extent of map (written to mapfile)
+MAPSERVER_EXTENT="-1.5831861262936526 52.4465003983706595 39.2608060398730458 71.7683216082912736"
+```
+
+...this is the contents of the `env-sample` file
+
+```bash
+$ ./run_PSILARTEMP.sh
+```
+This creates a Python virtualenv, installs all the Python dependencies, runs the model and stores output in a log file.
+
+Alternatively, primarily for development purposes, you can run the Python script PSILARTEMP directly:
+
+```bash
+$ ./PSILARTEMP.py
+```
-####Input data requirements
+#### Viewing the result of the model
-####Running the model
+**TODO** Add more details
-####Viewing the resault of the model
+
diff --git a/env-sample b/env-sample
index 033e7c4362f12b83a99870d01c44e2ae81c09837..d96ced325ca284ccc0f28227433f9bf67239cb8b 100644
--- a/env-sample
+++ b/env-sample
@@ -1,24 +1,23 @@
-# Use this as an example to create your own .env file
-
-# Where your application resides
-HOME_DIR=/home/foo/model/
-# Path to the weather data
-WEATHER_DATA_DIR=in/
-# The models start date
+# Use this example to create your own .env file
+# Path to this code (HOME_DIR + NAERSTADMO)
+HOME_DIR=/foobar/gridmodels/
+# Path to the weather data files. Expecting hourly values in files named met_1_0km_nordic-[YYYY-MM-DD].nc
+WEATHER_DATA_DIR=/foobar/met_1_0km_nordic/2024/
+# Start date for the model
START_DATE=2024-05-15
-# Path to optional CSV file with polygons for masking result.
+# Use this file to crop the output of the grid
MASK_FILE=Norge_landomrader.csv
-# Path to the output (GeoTIFF) files as seen from the running model code
-DATA_DIR=out/
-# Path to the generated mapfile as seen from the running model code
-MAPFILE_DIR=mapfile/
-# The path to the output (GeoTIFF files) as seen from Mapserver
-MAPSERVER_DATA_DIR=/foo/mapserver/data/SEPTREFHUM/
-# Where your generated MAPFILE and query templates should be placed
-MAPSERVER_MAPFILE_DIR=/foo/mapserver/wms/SEPTREFHUM/
-# Where mapserver logs for this WMS are written
-MAPSERVER_LOG_FILE=/foo/mapserver/log/SEPTREFHUM.log
-# Path to the temporary directory for writing temporary files and images. Must be writable by the user the web server is running as
-MAPSERVER_IMAGE_PATH=/foo/mapserver/tmp/
-# The value of the EXTENT parameter in Mapserver's mapfile. Units are DD (Decimal degrees)
-MAPSERVER_EXTENT="-1.5831861262936526 52.4465003983706595 39.2608060398730458 71.7683216082912736"
\ No newline at end of file
+# Where the GeoTIFF files will be output
+DATA_DIR=/foobar/mapserver/data/NAERSTADMO/
+# Where the mapfile will be output
+MAPFILE_DIR=/foobar/mapserver/wms/NAERSTADMO/
+# Path to the GeoTIFF files used by mapserver (written to mapfile)
+MAPSERVER_DATA_DIR=/foobar2/mapserver/data/NAERSTADMO/
+# Path to the mapfile used by mapserver (written to mapfile)
+MAPSERVER_MAPFILE_DIR=/foobar2/mapserver/wms/NAERSTADMO/
+# Path to the mapserver log file for this WMS (written to mapfile)
+MAPSERVER_LOG_FILE=/foobar2/mapserver/log/NAERSTADMO.log
+# Path for mapserver to store tmp images (written to mapfile)
+MAPSERVER_IMAGE_PATH=/foobar2/mapserver/tmp/
+# Extent of map (written to mapfile)
+MAPSERVER_EXTENT="-1.5831861262936526 52.4465003983706595 39.2608060398730458 71.7683216082912736"
diff --git a/mapfile/template.j2 b/mapfile/template.j2
index 0864d0f7f18ac0516568aed872eba67d42be17f2..372c040c90e9d8ee84ba099f81e430c803db979e 100644
--- a/mapfile/template.j2
+++ b/mapfile/template.j2
@@ -41,23 +41,31 @@ WEB
"wms_languages" "{{ language_codes|join(",")}}" # The first is the default
{% endif %}
- "wms_abstract.nb" "
+ "wms_abstract.nb" "<div id='preamble'>
<h2>Modellbeskrivelse</h2>
- <p>Modellen er laget av forsker Ragnhild Nærstad, på grunnlag av resultater fra forskingsprosjektet NORPHYT. Modellen beregner risiko for sporeproduksjon med påfølgende spredning, overlevelse og infeksjon på grunnlag av værdata. For at infeksjonen virkelig skal skje mådet være smitte til stede. </p>
- <p>Modellen er basert på forsøk over flere år hvor testplanter av potet, dyrket i veksthus, har blitt eksponert et døgn for smitte fra et potetfelt med tørrtåe på friland. </p>
- <p>Tørråteangrepet på disse testplantene har blitt sammenholdt med værforholdene dagen de ble eksponert, og basert på dette er det laget en modell. Modellen beregner hvor gunstig været er for sporeproduksjon med påfølgende sporespredning, overlevelse og infeksjon av sporene.</p>
- <h2>Tolking av varsel</h2>
- <p>Modellen er laget slik at risikotallene øker med angrepet på testplantene. Terskelverdien på 2,5 som gjør at varslet blir rødt, tilsvarer at det i gjennomsnitt ble funnet en tørråteflekk per testplante. Høye verdier betyr at værforholdene gir stor risiko for infeksjon hvis det er smitte til stede.</p>
+ <p>Kartet viser risiko for angrep av tørråte i potet. Modellen beregner hvor gunstig været er for spredning og infeksjon av tørråte-sporene. Det er størst fare for infeksjon ved varsel om angrep to eller flere dager etter hverandre, og når det er påvist smitte i området.</p>
+ <p>Varslene beregnes i rutenett a 1x1km basert på reanalyserte data og værprognoser fra Meteorologisk institutt. Varslene oppdateres en gang per døgn, med mulighet for å navigere i tid fra modellens startdato og inntil 2 døgn frem i tid.</p>
+ <p>Beregning av varsler startes 15.mai og avsluttes 15. oktober.</p>
+ </div>
+ <div id='body'>
+ Risiko for angrep er basert på <a href='https://www.vips-landbruk.no/forecasts/models/NAERSTADMO/' target='new'>Nærstads modell</a>. Nærstads modell beregnes også med data fra værstasjoner, hvor mer detaljerte beregninger kan hentes opp via visningen i kartet på VIPS-forsida.
+ </div>
"
- "wms_abstract.en" "
+ "wms_abstract.en" "<div id='preamble'>
<h2>Description of the model</h2>
- <p>The model is based on several years of experiments where trap plants have been placed next to a potato field infected with late blight. Infections on these plants have been correlated with weather conditions the day of exposure, and this is the data the model is based on. The model predicts if there are favorable conditions for spore production and the following spread, survival and infection of these spores. The model produces an infection risk, and a value of 2.5 corresponds to one spot of late blight on each trap plant exposed. This value of 2.5 is the threshold where the model issues a warning.</p>
+ <p>The map shows the risk of attack by Potato Late Blight. The model calculates how favourable the weather is for the spread and infection of the Late Blight spores. Ther isk of infection is at its highestt when an infection is predicted two or more days in a row, and when an infection has been confirmed detected in the area. </p>
+ <p>The warnings are calculated in a 1x1km grid based on reanalyzed data and weather forecasts from the Norwegian Meteorological Institute. The map is updated once per day, with the option to navigate in time from the model's start date and up to 2 days into the future. </p>
+ <p>Calculation of risk starts on 15 May and ends on 15 October.</p>
+ </div>
+ <div id='body'>
+ Infection risk is based on <a href='https://www.vips-landbruk.no/forecasts/models/NAERSTADMO/' target='new'>Nærstad's model</a>. Nærstad's model is also calculated with data from weather stations, where more detailed calculations can be retrieved via the display in the map on the VIPS front page.
+ </div>
"
"wms_enable_request" "*"
- "wms_title.en" "Potato Late Blight model "
- "wms_title.nb" "Potettørråte Nærstads model"
+ "wms_title.en" "Nærstad's model for Potato Late Blight"
+ "wms_title.nb" "Potettørråte - Nærstads model"
#"wms_onlineresource" "https://testvips.nibio.no/cgi-bin/NAERSTADMO"
"wms_getfeatureinfo_formatlist" "text/plain,text/html,text/xml"
"wms_accessconstraints" "none"
@@ -100,7 +108,8 @@ LAYER
STATUS ON
METADATA
- "wms_title.nb" " Potettørråte Nærstads model {{ timestep_date }}"
+ "wms_title.nb" "Potettørråte - Nærstads model {{ timestep_date }}"
+ "wms_title.en" "Potato Late Blight - Nærstad's model {{ timestep_date }}"
{% for language in languages %}
"wms_abstract.{{language.language_code}}" "
<ul style=\"list-style: none; padding: 0;\">
@@ -139,7 +148,7 @@ LAYER
END
END
CLASS
- NAME "Fare for angrep"
+ NAME "Stor fare for angrep"
EXPRESSION ([pixel] >= 4)
STYLE
COLOR 255 0 0
@@ -159,11 +168,12 @@ END # Layer
STATUS ON
METADATA
- "wms_title" " Potettørråte Nærstads model risiko {{ timestep_date }}"
+ "wms_title.nb" "Potettørråte - Nærstads model infeksjonsrisiko {{ timestep_date }}"
+ "wms_title.en" "Potato Late Blight - Nærstad's model infection risk {{ timestep_date }}"
{% for language in languages %}
"wms_abstract.{{language.language_code}}" "
<ul style=\"list-style: none; padding: 0;\">
- <li style=\"margin-bottom: 5px;\"><span style=\"display: inline-block; width: 25px; background: linear-gradient(to right, #0000FF, #FF0000);\"> </span> {{language.day_degrees}}</li>
+ <li style=\"margin-bottom: 5px;\"><span style=\"display: inline-block; width: 25px; background: linear-gradient(to right, #0000FF, #FF0000);\"> </span> {{language.risk}}</li>
</ul>
"
{% endfor %}
@@ -187,40 +197,6 @@ END # Layer
END
END
-END # Layer
-
- LAYER
- NAME "NAERSTADMO.IR.{{ timestep_date }}"
- DATA "{{mapserver_data_dir}}IR_result_{{ timestep_date }}.tif"
- TEMPLATE "{{mapserver_mapfile_dir}}query_template_IR.xml" TOLERANCE 1 TOLERANCEUNITS PIXELS
- TYPE RASTER
- #PROCESSING "BANDS=1" # IR band on top (others invisible, but band values are available in the query template)
- #PROCESSING "SCALE=AUTO"
- #PROCESSING "NODATA=-1"
-
-
- STATUS ON
- METADATA
- "wms_title" "Potettørråte Nærstads model infeksjonsrisiko {{ timestep_date }}"
- {% for language in languages %}
- "wms_abstract.{{language.language_code}}" "
- <ul style=\"list-style: none; padding: 0;\">
- <li style=\"margin-bottom: 5px;\"><span style=\"display: inline-block; width: 25px; background: linear-gradient(to right, #0000FF, #FF0000);\"> </span> {{language.day_degrees}}</li>
- </ul>
- "
- {% endfor %}
-
- END
- CLASSITEM "[pixel]"
- CLASS
- NAME "IR [0-1]"
- EXPRESSION ([pixel] >= 0 AND [pixel] <= 1)
- STYLE
- DATARANGE 0 1
- COLORRANGE 255 255 0 0 0 255
- END
- END
-
END # Layer
{% endfor %}
diff --git a/run_NAERSTADMO.sh b/run_NAERSTADMO.sh
index 6f0b8777f3f89bf84aa28875153079552daea767..f25253d424ed5b1c01e512781d9cf57c898bfe42 100755
--- a/run_NAERSTADMO.sh
+++ b/run_NAERSTADMO.sh
@@ -53,8 +53,8 @@ cd $APP_PATH
# Create and activate the virtual environment
python3 -m venv .venv
. .venv/bin/activate
-python3 -m pip install --upgrade pip
-pip install -r $REQUIREMENTS
+python3 -m pip install -q --upgrade pip
+pip install -q -r $REQUIREMENTS
# Run the model
echo "==== `date`: Running model" &>> "$LOG_FILE"
diff --git a/wms_illustration.png b/wms_illustration.png
new file mode 100644
index 0000000000000000000000000000000000000000..2cc29fe3bf0f06d26f591203ab4589b6ecd9d100
Binary files /dev/null and b/wms_illustration.png differ