From 79d760786cec8bba04507d068fd0659a36e5ab39 Mon Sep 17 00:00:00 2001
From: cemachelen <h.l.burns@leeds.ac.uk>
Date: Wed, 20 Mar 2019 15:33:35 +0000
Subject: [PATCH 1/2] :truck: tidy up for master branch

---
 Python/__pycache__/maptoolkit.cpython-37.pyc | Bin 13338 -> 0 bytes
 Python/analysis_tools/pmap.py                | 109 -------------------
 Python/analysis_tools/pmap_plot.py           |  85 ---------------
 Python/{ => comming_soon}/genmaps.py         |   0
 Python/{ => comming_soon}/maptoolkit.py      |   0
 Python/maptoolkit.pyc                        | Bin 15415 -> 0 bytes
 tools/README.md                              |   6 -
 tools/michael_archive.sh                     |  48 --------
 8 files changed, 248 deletions(-)
 delete mode 100644 Python/__pycache__/maptoolkit.cpython-37.pyc
 delete mode 100755 Python/analysis_tools/pmap.py
 delete mode 100644 Python/analysis_tools/pmap_plot.py
 rename Python/{ => comming_soon}/genmaps.py (100%)
 rename Python/{ => comming_soon}/maptoolkit.py (100%)
 delete mode 100644 Python/maptoolkit.pyc
 delete mode 100644 tools/README.md
 delete mode 100755 tools/michael_archive.sh

diff --git a/Python/__pycache__/maptoolkit.cpython-37.pyc b/Python/__pycache__/maptoolkit.cpython-37.pyc
deleted file mode 100644
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diff --git a/Python/analysis_tools/pmap.py b/Python/analysis_tools/pmap.py
deleted file mode 100755
index 98c9657..0000000
--- a/Python/analysis_tools/pmap.py
+++ /dev/null
@@ -1,109 +0,0 @@
-#!/usr/bin/env python3
-# -*- coding: utf-8 -*-
-"""pmaps
-.. module:: genmaps
-    :platform: Unix
-    :synopis:
-.. moduleauther: CEMAC (UoL)
-.. description: This module was developed by CEMAC as part of the UNRESP
-   Project. This Script plots CALPUFF concrec data on a map.
-   :copyright: © 2019 University of Leeds.
-   :license: BSD-2 Clause.
-Example:
-    To use::
-        ./genemaps.py <date>
-        <date> - Date string, format YYYYMMDD, of the current CALPUFF run.
-                 Used to locate directory containing the SO2 output files
-                 (with assumed naming convention 'concrec0100**.dat',
-                  where '**' goes from '01' through to '48')
-.. CEMAC_UNRESPForcastingSystem:
-   https://github.com/cemac/UNRESPForcastingSystem
-"""
-from __future__ import print_function
-import argparse
-from dateutil.parser import parse
-import datetime
-from maptoolkit import *
-import netCDF4
-
-
-def conc_array_plain(ny, nx, filePaths):
-    # Read in concentration data:
-    f = open(filePaths, 'r')
-    lines = f.read().splitlines()
-    f.close
-    # Process concentration data into desired format:
-    conc = np.array([float(X) for X in lines]) * 100**3  # ug/cm^3 -> ug/m^3
-    concAry = np.reshape(conc, (ny, nx))  # Reshape data onto latlon grid
-    return concAry, conc
-
-
-# READ IN COMMAND LINE ARGUMENTS
-dstring = ("Date string, format YYYYMMDD, START date and End Date")
-parser = argparse.ArgumentParser(description=dstring)
-parser.add_argument("--start", help=dstring, type=str)
-parser.add_argument("--end", help=dstring, type=str)
-args = parser.parse_args()
-
-# Required files and info
-start = datetime.datetime.strptime(args.start, "%Y%m%d")
-end = datetime.datetime.strptime(args.end, "%Y%m%d")
-datahome = "/nfs/see-fs-01_users/earhbu/UNRESP_SPACE/UNRESPForecastingSystem/"
-nConcFiles = 48
-binLims = [10, 350, 600, 2600, 9000, 14000]  # SO2 bin limits
-xyFile = "../data/xy_masaya.dat"
-glat, glon, latMin, latMax, lonMin, lonMax, ny, nx = genxy(xyFile)
-datelist = [start + datetime.timedelta(days=x) for x in range(0, (end-start).days)]
-"""
-the probability is simply calculated by checking each single hourly file and
-"counting" how many time the concentration in each grid point is over a
-specific threshold (here 100 micrograms/m3). This number (obtained for each
-grid point) is then normalized over the total number of simulated hours."""
-
-threshold = 100
-
-nhours = 0
-countersum = np.zeros((ny, nx))
-concAsum = np.zeros((ny, nx))
-concsum = np.zeros(18000)
-concsumcount = np.zeros(18000)
-for date in datelist:
-    month = str(date.strftime("%Y%m"))
-    try:
-        concDir = datahome + "CALPUFF_OUT/CALPUFF/m" + month + '/' + str(date.strftime("%Y%m%d"))
-        filenames, filePaths = concfiles(nConcFiles, concDir, SOX='SO2')
-    except AssertionError:
-        print(concDir + "does not exist skipping")
-        continue
-    for i, fname in enumerate(filePaths):
-        nhours += 1  # number of simulated hours
-        concA, concx = conc_array(ny, nx, fname, binLims)
-        counter = np.zeros_like(concA)
-        counter[concA >= 100] = 1
-        concAsum = concAsum + concA
-        countersum = counter + countersum
-        concsum = concx + concsum
-        c = np.zeros(18000)
-        c[concx>=100] = 1
-        concsumcount = c + concsumcount
-# Write Netcdf out
-f = netCDF4.Dataset('conc.nc', 'w')
-f.createDimension('lon', nx)
-f.createDimension('lat', ny)
-f.createDimension('N', 1)
-f.createDimension('points', 18000)
-h2 = f.createVariable('count', 'float', ('lon', 'lat'))
-h2[:] = countersum
-h1 = f.createVariable('conc', 'float', ('lon', 'lat'))
-h1[:] = concAsum
-h3 = f.createVariable('long', 'float', ('lon'))
-h3[:] = glon[0, :]
-h4 = f.createVariable('lati', 'float', ('lat'))
-h4[:] = glat[:, 0]
-h5 = f.createVariable('nhours', 'float', ('N'))
-h5[:] = nhours
-h6 = f.createVariable('concpoint', 'float', ('points'))
-h6[:] = concsum
-h7 = f.createVariable('countpoints', 'float', ('points'))
-h7[:] = concsumcount
-f.close()
diff --git a/Python/analysis_tools/pmap_plot.py b/Python/analysis_tools/pmap_plot.py
deleted file mode 100644
index 6506cfd..0000000
--- a/Python/analysis_tools/pmap_plot.py
+++ /dev/null
@@ -1,85 +0,0 @@
-import netCDF4
-import numpy as np
-import matplotlib.pyplot as plt
-import matplotlib.image as mpimg
-from mpl_toolkits.mplot3d import axes3d
-import matplotlib as mpl
-from mpl_toolkits.basemap import Basemap
-from matplotlib.font_manager import FontProperties
-import os
-import datetime as dt
-import pytz
-import utm
-import gmplot
-import cartopy.crs as ccrs
-import cartopy.io.img_tiles as cimgt
-import cartopy
-import cartopy.feature as cfeat
-from cartopy.mpl.gridliner import LONGITUDE_FORMATTER, LATITUDE_FORMATTER
-import netCDF4
-from dateutil.parser import parse
-from maptoolkit import *
-file2read = netCDF4.Dataset('conc.nc', 'r')
-lat = file2read.variables['lati'][:]
-lon = file2read.variables['long'][:]
-nhours = file2read.variables['nhours'][:]
-count = file2read.variables['countpoints'][:]
-datahome = "/nfs/see-fs-01_users/earhbu/UNRESP_SPACE/UNRESPForecastingSystem/"
-nConcFiles = 48
-binLims = [10, 350, 600, 2600, 9000, 14000]  # SO2 bin limits
-xyFile = "../data/xy_masaya.dat"
-glat, glon, latMin, latMax, lonMin, lonMax, ny, nx = genxy(xyFile)
-plt.figure(figsize=(16, 12))
-im = gen_im(lonMin, latMin, lonMax, latMax, imtype="World_Shaded_Relief",)
-so2title = (r'june 2018 - feb 2019. probability greater than 100ug/m$^3$'+' \n (cut off reduced to 0.001)')
-bmap = Basemap(llcrnrlon=lonMin, llcrnrlat=latMin,
-               urcrnrlon=lonMax, urcrnrlat=latMax)
-bmap.imshow(im, origin='upper')
-concAry = np.reshape(count, (ny, nx))
-#concAry[concAry < 0.05] = np.nan
-concmap = concAry / nhours*100
-concmap = np.ma.masked_array(concmap, concmap < 0.001)
-bmap.contourf(glon, glat, concmap, cmap=plt.cm.plasma_r)
-cbar = bmap.colorbar(location='bottom', pad='20%', extend='both', extendfrac='auto', cmap=plt.cm.plasma_r)
-cbar.set_label(label=('probability %'), fontsize=18)
-cbar.ax.tick_params(labelsize=16)
-cbar.solids.set(alpha=1)
-latTicks = np.arange(round(latMin, 1), round(latMax, 1) + 0.1, 0.1)
-lonTicks = np.arange(round(lonMin, 1), round(lonMax, 1) + 0.1, 0.2)
-bmap.drawparallels(latTicks, labels=[1, 0, 0, 0], linewidth=0.0,
-                   fontsize=16)
-bmap.drawmeridians(lonTicks, labels=[0, 0, 0, 1], linewidth=0.0,
-                   fontsize=16)
-towns = (' El Panama', ' Rigoberto', ' Pacaya', ' El Crucero',
-         ' La Concepcion', ' Masaya', ' San Marcos',
-         ' San Rafael del Sur', ' Diriamba', ' Jinotepe',
-         ' Masatepe')
-townCoords = ((-86.2058, 11.972), (-86.2021, 11.9617),
-                (-86.3013, 11.9553), (-86.3113, 11.9923),
-                (-86.189772, 11.936161), (-86.096053, 11.973523),
-                (-86.20317, 11.906584), (-86.43639, 11.847034),
-                (-86.239592, 11.85632), (-86.19993, 11.85017),
-                (-86.143758, 11.91512))
-cities = (' MANAGUA',)
-cityCoords = ((-86.29, 12.12),)
-volcCoords = (-86.1608, 11.9854)
-font = FontProperties()
-font.set_weight('bold')
-font.set_family('monospace')
-tc='k'
-for i, town in enumerate(towns):
-    plt.plot(townCoords[i][0], townCoords[i]
-             [1], 'ok', markersize=4)
-    plt.text(townCoords[i][0], townCoords[i][1], town,
-             color=tc, fontproperties=font, fontsize=12)
-for i, city in enumerate(cities):
-    plt.plot(cityCoords[i][0], cityCoords[i]
-             [1], 'sk', markersize=6)
-    plt.text(cityCoords[i][0], cityCoords[i][1], city,
-             fontproperties=font, fontsize=16)
-font0 = FontProperties()
-font0.set_family('monospace')
-plt.plot(volcCoords[0], volcCoords[1], '^r', markersize=6)
-plt.suptitle(so2title, fontsize=24)
-plt.savefig('test.png', dpi=250)
-plt.close()
diff --git a/Python/genmaps.py b/Python/comming_soon/genmaps.py
similarity index 100%
rename from Python/genmaps.py
rename to Python/comming_soon/genmaps.py
diff --git a/Python/maptoolkit.py b/Python/comming_soon/maptoolkit.py
similarity index 100%
rename from Python/maptoolkit.py
rename to Python/comming_soon/maptoolkit.py
diff --git a/Python/maptoolkit.pyc b/Python/maptoolkit.pyc
deleted file mode 100644
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diff --git a/tools/README.md b/tools/README.md
deleted file mode 100644
index 1f123a5..0000000
--- a/tools/README.md
+++ /dev/null
@@ -1,6 +0,0 @@
-# TOOLS
-
-Bash tools for operational Forecasting.
-
-* Archiving (under development)
-  * micahel_archive.sh (example of automated archiving - need to add in options and generise)
diff --git a/tools/michael_archive.sh b/tools/michael_archive.sh
deleted file mode 100755
index 7c1e364..0000000
--- a/tools/michael_archive.sh
+++ /dev/null
@@ -1,48 +0,0 @@
-#!/bin/bash -
-#title          :michael_archive.sh
-#description    :Archive IMO output for michael
-#author         :CEMAC - Helen
-#date           :20190304
-#version        :0.1-beta
-#usage          :./michael_archive.sh
-#notes          :
-#bash_version   :4.2.46(2)-release
-#============================================================================
-# A stand alone archiving script to extract and reformat the UNRESP data
-archive="/ds/shared/Earth&Environment/Research/SEE/Research-1/UNRESP/Image_archive/"
-new=/nfs/earcemac/projects/unresp_for_michael
-cd $new
-mkdir 2017
-mkdir 2018
-cd 2017
-for i in $(seq -f "%02g" 1 12)
-  do
-    mkdir m2017$i
-  done
-cd ../2018
-for i in $(seq -f "%02g" 1 12)
-  do
-    mkdir m2018$i
-  done
-cd $archive/2018
-for d in */; do
-    md=${d:(-5)}
-    m=${md:(0):(2)}
-    folder=$new/2018/m2018$m/20$d
-    if [ ! -e $folder ]
-    then
-      mkdir $folder
-    fi
-    cp -p $d/calpuff_so2_masaya/concrec*.dat $folder
-done
-cd $archive/2017
-for d in */; do
-    md=${d:(-5)}
-    m=${md:(0):(2)}
-    folder=$new/2017/m2017$m/20$d
-    if [ ! -e $folder ]
-    then
-      mkdir $folder
-    fi
-    cp -p $d/calpuff_so2_masaya/concrec*.dat $folder
-done

From d2c81d690a4b530878669b16a86090c29f9bd12d Mon Sep 17 00:00:00 2001
From: Helen Burns <H.L.Burns@leeds.ac.uk>
Date: Wed, 20 Mar 2019 16:00:54 +0000
Subject: [PATCH 2/2] :pencil2: missing git clone command address

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 6c5a6b2..21738de 100644
--- a/README.md
+++ b/README.md
@@ -41,7 +41,7 @@ Non anaconda installations require a separate build of ecCodes python API:
 Anaconda python, unix systems (recommended)
 
 ```
-git clone
+git clone https://github.com/cemac/UNRESPForecastingSystem.git
 cd UNRESPForecastingSystem
 conda env create -f environment.yml
 ```