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rrrReader.py
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rrrReader.py
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# -*- coding: utf-8 -*-
"""
/***************************************************************************
rrrReader
A QGIS plugin
Reads RRR files
Generated by Plugin Builder: http://g-sherman.github.io/Qgis-Plugin-Builder/
-------------------
begin : 2024-02-28
git sha : $Format:%H$
copyright : (C) 2024 by Morten Sickel
email : morten@sickel.net
***************************************************************************/
/***************************************************************************
* *
* This program 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 2 of the License, or *
* (at your option) any later version. *
* *
***************************************************************************/
"""
from qgis.PyQt.QtCore import QSettings, QTranslator, QCoreApplication
from qgis.PyQt.QtGui import QIcon
from qgis.PyQt.QtWidgets import QAction
from qgis.core import QgsVectorLayer, QgsFeature, QgsField, QgsGeometry, QgsPointXY, QgsField, QgsProject, QgsMapLayerProxyModel, QgsCoordinateTransform, QgsCoordinateReferenceSystem
from PyQt5.QtCore import *
# Initialize Qt resources from file resources.py
from .resources import *
# Import the code for the dialog
from .rrrReader_dialog import rrrReaderDialog
import os.path
import json
import re
class rrrReader:
"""QGIS Plugin Implementation."""
def __init__(self, iface):
"""Constructor.
:param iface: An interface instance that will be passed to this class
which provides the hook by which you can manipulate the QGIS
application at run time.
:type iface: QgsInterface
"""
# Save reference to the QGIS interface
self.iface = iface
# initialize plugin directory
self.plugin_dir = os.path.dirname(__file__)
# initialize locale
locale = QSettings().value('locale/userLocale')[0:2]
locale_path = os.path.join(
self.plugin_dir,
'i18n',
'rrrReader_{}.qm'.format(locale))
if os.path.exists(locale_path):
self.translator = QTranslator()
self.translator.load(locale_path)
QCoreApplication.installTranslator(self.translator)
# Declare instance attributes
self.actions = []
self.menu = self.tr(u'&Spectral data')
# Check if plugin was started the first time in current QGIS session
# Must be set in initGui() to survive plugin reloads
self.first_start = None
# noinspection PyMethodMayBeStatic
def tr(self, message):
"""Get the translation for a string using Qt translation API.
We implement this ourselves since we do not inherit QObject.
:param message: String for translation.
:type message: str, QString
:returns: Translated version of message.
:rtype: QString
"""
# noinspection PyTypeChecker,PyArgumentList,PyCallByClass
return QCoreApplication.translate('rrrReader', message)
def add_action(
self,
icon_path,
text,
callback,
enabled_flag=True,
add_to_menu=True,
add_to_toolbar=False,
status_tip=None,
whats_this=None,
parent=None):
"""Add a toolbar icon to the toolbar.
:param icon_path: Path to the icon for this action. Can be a resource
path (e.g. ':/plugins/foo/bar.png') or a normal file system path.
:type icon_path: str
:param text: Text that should be shown in menu items for this action.
:type text: str
:param callback: Function to be called when the action is triggered.
:type callback: function
:param enabled_flag: A flag indicating if the action should be enabled
by default. Defaults to True.
:type enabled_flag: bool
:param add_to_menu: Flag indicating whether the action should also
be added to the menu. Defaults to True.
:type add_to_menu: bool
:param add_to_toolbar: Flag indicating whether the action should also
be added to the toolbar. Defaults to True.
:type add_to_toolbar: bool
:param status_tip: Optional text to show in a popup when mouse pointer
hovers over the action.
:type status_tip: str
:param parent: Parent widget for the new action. Defaults None.
:type parent: QWidget
:param whats_this: Optional text to show in the status bar when the
mouse pointer hovers over the action.
:returns: The action that was created. Note that the action is also
added to self.actions list.
:rtype: QAction
"""
icon = QIcon(icon_path)
action = QAction(icon, text, parent)
action.triggered.connect(callback)
action.setEnabled(enabled_flag)
if status_tip is not None:
action.setStatusTip(status_tip)
if whats_this is not None:
action.setWhatsThis(whats_this)
if add_to_toolbar:
# Adds plugin icon to Plugins toolbar
self.iface.addToolBarIcon(action)
if add_to_menu:
self.iface.addPluginToVectorMenu(
self.menu,
action)
self.actions.append(action)
return action
def initGui(self):
"""Create the menu entries and toolbar icons inside the QGIS GUI."""
icon_path = ':/plugins/rrrReader/icon.png'
self.add_action(
icon_path,
text=self.tr(u'Load RRR-files'),
callback=self.run,
parent=self.iface.mainWindow())
# will be set False in run()
self.first_start = True
def unload(self):
"""Removes the plugin menu item and icon from QGIS GUI."""
for action in self.actions:
self.iface.removePluginVectorMenu(
self.tr(u'&Spectral data'),
action)
self.iface.removeToolBarIcon(action)
def newlayer(self):
layername = 'rrr-data'
CRS= QgsProject.instance().crs()
vl = QgsVectorLayer("Point", layername, "memory",crs=CRS)
pr = vl.dataProvider()
# Enter editing mode
vl.startEditing()
# is this needed?
# add fields
pr.addAttributes( [
QgsField("fid",QVariant.Int),
QgsField("rrr", QVariant.String),
QgsField("rrr_data", QVariant.String),
QgsField("filename", QVariant.String),
QgsField("osi_relevant", QVariant.Int),
QgsField("sample_id", QVariant.String),
QgsField("sample_type", QVariant.String),
QgsField("mission_code", QVariant.String),
QgsField("bar_code", QVariant.String)
])
# filename and mission should be kept as the two last fields
# as they will be added on later
# when the data is collected
# Commit changes - is this needed?
vl.commitChanges()
# To display the new layer in the project
QgsProject.instance().addMapLayer(vl)
# Set the new layer as the default layer to import data into
self.dlg.cbMapLayer.setLayer(vl)
def run(self):
"""Run method that performs all the real work"""
# Create the dialog with elements (after translation) and keep reference
# Only create GUI ONCE in callback, so that it will only load when the plugin is started
if self.first_start == True:
self.first_start = False
self.dlg = rrrReaderDialog(parent=self.iface.mainWindow())
# This makes the dialog modal
# self.dlg.pbLoadData.clicked.connect(self.selectfile)
self.dlg.pbNewLayer.clicked.connect(self.newlayer)
self.dlg.cbMapLayer.setFilters(QgsMapLayerProxyModel.PointLayer)
# show the dialog
self.dlg.show()
# Run the dialog event loop
result = self.dlg.exec_()
# See if OK was pressed
if result:
# Do something useful here - delete the line containing pass and
# substitute with your code.
filename=self.dlg.fwRRRFile.filePath()
print(filename)
if self.dlg.cbAllFiles.isChecked():
directory=os.path.split(filename)[0]
files=os.listdir(directory)
rrrfiles=list(filter(lambda x: x.startswith('rrr_'), files))
rrrfiles.sort()
for filename in rrrfiles:
self.readFile(directory+'/'+filename)
else:
self.readFile(filename)
self.iface.mapCanvas().refreshAllLayers()
def readFile(self,filename):
print(f'reading {filename}')
lat = None
lon = None
osirelevantfound = False
sampleid = None
rrr_data = {}
rrr_data['osinuclides'] = {}
rrr_data['nuclides'] = {}
rrr_data['attributes'] = {}
#filename = "C:/Users/morten/rrr_244 (002).txt"
layer=self.dlg.cbMapLayer.currentLayer()
#layer = QgsProject.instance().mapLayersByName('rrr')[0]
pr = layer.dataProvider()
rrr = open(filename,'r').read()
attributes = {}
readquantified = False
lines = rrr.split('\n')
print(f'{len(lines)} lines read')
header = None
fromCRS=QgsCoordinateReferenceSystem("EPSG:4326")
# The coordinate system the data to be imported are stored in
toCRS= layer.crs()
self.transformation = QgsCoordinateTransform(fromCRS, toCRS, QgsProject.instance())
readosi = False
osisfound = []
for idx,line in enumerate(lines):
line = line.strip()
if line.startswith('--------------------------'):
header = lines[idx-1].lower()
print(header)
continue
if line.endswith('=============='):
parts = line.split(' ')
del parts[-1]
header = ' '.join(parts).lower()
print(header)
if header == 'sample information':
if sampleid is None and line.startswith('Sample ID:'):
data = re.split(r"\s{2,}",line)
sampleid = data[1]
print(f'Sample ID: {sampleid}')
continue
if line.startswith('OSI_'):
try:
print(idx,line)
if ' ' in line:
(k,v) = line.split(' ',1)
else:
k = line
v = lines[idx+1]
(OSI,k) = k.split('_')
k = k.strip()
v = v.strip()
if k == 'Lat':
lat = float(v)
if k == 'Lon':
lon = float(v)
print(k,v)
attributes[k] = v
except IndexError as e:
print(line,idx)
print(e)
continue
#if header == 'Activity Summary':
if line.lower().startswith('detected'):
# acttype = line
# continue
readosi = ' OSI ' in line
if readquantified or line == 'Nuclides Quantified:':
if line.startswith('Nuclide'):
if line == 'Nuclides Quantified:':
readquantified = True
continue
else:
headers = re.split(r"\s{2,}",line)
continue
elif line.endswith(':'):
readquantified = False
continue
data = re.split(r"\s{2,}",line)
if len(data) > 2:
line = {}
for idx,head in enumerate(headers):
line[head]=data[idx]
rrr_data['nuclides'][line['Nuclide']] = line
if readosi:
if line.lower().startswith('nuclide'):
headers = re.split(r"\s{2,}",line)
continue
data = re.split(r"\s{2,}",line)
if len(data) > 2:
linedata = {}
for idx,head in enumerate(headers):
linedata[head]=data[idx]
rrr_data['osinuclides'][linedata['Nuclide']] = linedata
if not (lat is None or lon is None):
osirelevantfound = len(rrr_data['osinuclides']) > 0
rrr_data['attributes'] = attributes
insdata = [None,rrr,json.dumps(rrr_data),filename,osirelevantfound,sampleid,attributes['SampleType'],attributes['MissionCode'],attributes['BarCode']]
feature = QgsFeature()
point=QgsPointXY(float(lon),float(lat))
prpoint=self.transformation.transform(point)
geom=QgsGeometry.fromPointXY(prpoint)
feature.setGeometry(geom)
# Fixes attibs later:
feature.setAttributes(insdata)
pr.addFeatures( [ feature ] )