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Unverified Commit 6f50bc0c authored by jdha's avatar jdha Committed by GitHub
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Merge pull request #1 from jdha/PyNEMO3 

Py nemo3
parents b1ee0b2f a666111c
master
1 merge request!49update a few files
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Showing with 293 additions and 436 deletions
DESCRIPTION.rst 0 → 100644
View file @ 6f50bc0c
PyNEMO Description
===================
\ No newline at end of file
pynemo/gui/nemo_bdy_input_window.py
View file @ 6f50bc0c
......@@ -6,13 +6,13 @@ Created on 21 Jan 2015
# pylint: disable=E1103
# pylint: disable=no-name-in-module
# pylint: disable=E1002
from PyQt4 import QtGui
from PyQt5 import QtGui, QtWidgets
from .nemo_bdy_namelist_edit import NameListEditor
from .nemo_bdy_mask_gui import MatplotlibWidget
from PyQt4.QtGui import QSizePolicy
from PyQt4.Qt import Qt
from PyQt5.QtWidgets import QSizePolicy
from PyQt5.Qt import Qt
class InputWindow(QtGui.QDialog):
class InputWindow(QtWidgets.QDialog):
'''
Input Window for editing pyNEMO settings
'''
......@@ -43,15 +43,15 @@ class InputWindow(QtGui.QDialog):
self.mpl_widget.set_mask_settings(float(setup.settings['mask_max_depth']), float(setup.settings['mask_shelfbreak_dist']))
splitter = QtGui.QSplitter(Qt.Horizontal)
splitter = QtWidgets.QSplitter(Qt.Horizontal)
splitter.addWidget(self.nl_editor)
splitter.addWidget(self.mpl_widget)
hbox = QtGui.QHBoxLayout()
hbox = QtWidgets.QHBoxLayout()
hbox.addWidget(splitter)
self.setLayout(hbox)
#set the Dialog title
self.setWindowTitle("PyNEMO Settings Editor")
QtGui.QApplication.setStyle(QtGui.QStyleFactory.create('Cleanlooks'))
QtWidgets.QApplication.setStyle(QtWidgets.QStyleFactory.create('Cleanlooks'))
#show the window
self.show()
pynemo/gui/nemo_bdy_mask.py
View file @ 6f50bc0c
......@@ -12,8 +12,8 @@ import logging
from scipy import ndimage
import matplotlib.pyplot as plt
from pynemo.utils import gcoms_break_depth
from PyQt4.QtGui import QMessageBox
from PyQt4 import QtCore
from PyQt5.QtWidgets import QMessageBox
from PyQt5 import QtCore
class Mask(object):
"""This is a Mask holder. which reads from a netCDF bathymetry file and
......@@ -199,7 +199,7 @@ class Mask(object):
mask_data[index] = self.data[index]
#connected components
label_mask, num_labels = ndimage.label(mask_data)
mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,range(1, num_labels+1))
mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,list(range(1, num_labels+1)))
max_area_mask = None
if mean_values.size != 0:
max_area_index = np.argmax(mean_values)+1
......@@ -228,7 +228,7 @@ class Mask(object):
label_mask, num_labels = ndimage.label(mask_data)
if num_labels == 0: #if mask is empty/clear
return
mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,range(1, num_labels+1))
mean_values = ndimage.sum(np.ones(self.data.shape),label_mask,list(range(1, num_labels+1)))
max_area_mask = None
if mean_values.size != 0:
max_area_index = np.argmax(mean_values)+1
......
pynemo/gui/nemo_bdy_mask_gui.py
View file @ 6f50bc0c
......@@ -10,15 +10,15 @@ from mpl_toolkits.basemap import Basemap, cm
import numpy as np
from .selection_editor import PolygonEditor, BoxEditor
import os.path
from PyQt4.QtCore import pyqtSignal, pyqtSlot, Qt
from nemo_bdy_mask import Mask
from PyQt5.QtCore import pyqtSignal, pyqtSlot, Qt
from .nemo_bdy_mask import Mask
import logging
from PyQt4.QtGui import QSizePolicy
from PyQt5.QtWidgets import QSizePolicy
from matplotlib.colors import Normalize
mask_alpha = 0.3
from PyQt4 import QtGui
from PyQt5 import QtGui, QtWidgets
import matplotlib.pyplot as plt
from matplotlib.figure import Figure
from matplotlib.path import Path
......@@ -26,7 +26,7 @@ from matplotlib.transforms import Bbox
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.backends.backend_qt4agg import NavigationToolbar2QT as NavigationToolbar
# pylint: disable=E1002
class MatplotlibWidget(QtGui.QWidget):
class MatplotlibWidget(QtWidgets.QWidget):
"""This class is a QWidget for pyNEMO mask plot"""
min_depth = 200.0
shelfbreak_dist = 200.0
......@@ -34,7 +34,7 @@ class MatplotlibWidget(QtGui.QWidget):
def __init__(self, parent=None, mask=None, min_depth = 200.0, shelfbreak_dist = 200.0,*args, **kwargs):
""" Initialises the mask, matplot and the navigation toolbar """
super(MatplotlibWidget, self).__init__(parent)
#QtGui.QWidget.__init__(self, parent)
#QtWidgets.QWidget.__init__(self, parent)
self.figure = Figure(*args, **kwargs)
self.canvas = FigureCanvas(self.figure)
self.mask = mask
......@@ -51,7 +51,7 @@ class MatplotlibWidget(QtGui.QWidget):
self.toolbar.drawing_tool.connect(self.drawing_tool_callback)
self.axes = self.figure.add_subplot(111)
self.cbar = None
layout = QtGui.QVBoxLayout()
layout = QtWidgets.QVBoxLayout()
layout.addWidget(self.toolbar)
layout.addWidget(self.canvas)
self.setLayout(layout)
......@@ -126,7 +126,7 @@ class MatplotlibWidget(QtGui.QWidget):
x = np.arange(0, self.mask.lon.shape[0])
y = np.arange(0, self.mask.lon.shape[1])
x_vals, y_vals = np.meshgrid(y, x)
grid = zip(x_vals.ravel(), y_vals.ravel())
grid = list(zip(x_vals.ravel(), y_vals.ravel()))
self._drawing_tool.polygon.set_linewidth(1.0)
p_path = Path(self._drawing_tool.polygon.xy)
......@@ -146,7 +146,7 @@ class MatplotlibWidget(QtGui.QWidget):
x = np.arange(0, self.mask.lon.shape[0])
y = np.arange(0, self.mask.lon.shape[1])
x_vals, y_vals = np.meshgrid(y, x)
grid = zip(x_vals.ravel(), y_vals.ravel()) #check for the index
grid = list(zip(x_vals.ravel(), y_vals.ravel())) #check for the index
self._drawing_tool.polygon.set_linewidth(1.0)
p_path = Path(self._drawing_tool.polygon.xy)
......
pynemo/gui/nemo_bdy_mask_gui.py.interactive_cbar
View file @ 6f50bc0c
......@@ -10,10 +10,10 @@ from mpl_toolkits.basemap import Basemap, cm
import numpy as np
from .selection_editor import PolygonEditor, BoxEditor
import os.path
from PyQt4.QtCore import pyqtSignal, pyqtSlot, Qt
from PyQt5.QtCore import pyqtSignal, pyqtSlot, Qt
from nemo_bdy_mask import Mask
import logging
from PyQt4.QtGui import QSizePolicy
from PyQt5.QtGui import QSizePolicy
mask_alpha = 0.3
......
pynemo/gui/nemo_bdy_namelist_edit.py
View file @ 6f50bc0c
......@@ -6,13 +6,14 @@ Editor for namelist.bdy file
# pylint: disable=E1103
# pylint: disable=no-name-in-module
# pylint: disable=E1002
from PyQt4 import QtGui, QtCore
from PyQt4.QtCore import pyqtSignal, Qt, QRect, QPoint
from PyQt5 import QtGui, QtCore, QtWidgets
from PyQt5.QtCore import pyqtSignal, Qt, QRect, QPoint
import ast
from PyQt4.QtGui import QMessageBox, QRegion, QIcon, QToolTip, QCursor
from PyQt5.QtGui import QRegion, QIcon, QCursor
from PyQt5.QtWidgets import QMessageBox, QToolTip
class NameListEditor(QtGui.QWidget):
class NameListEditor(QtWidgets.QWidget):
'''
This class creates a gui for the Namelist file options
'''
......@@ -34,25 +35,25 @@ class NameListEditor(QtGui.QWidget):
'''
Initialises the UI components of the GUI
'''
client = QtGui.QWidget(self)
client = QtWidgets.QWidget(self)
# Create the Layout to Grid
grid = QtGui.QGridLayout()
grid = QtWidgets.QGridLayout()
# Loop through the settings and create widgets for each setting
index = 0
for setting in self.settings:
# initialises setting Widget
label = QtGui.QLabel(setting)
qlabel = QtGui.QPushButton("")
qlabel.setIcon(self.style().standardIcon(QtGui.QStyle.SP_MessageBoxQuestion))
label = QtWidgets.QLabel(setting)
qlabel = QtWidgets.QPushButton("")
qlabel.setIcon(self.style().standardIcon(QtWidgets.QStyle.SP_MessageBoxQuestion))
if type(self.settings[setting]).__name__ in ['str', 'float', 'double',
'int', 'time', 'dict']:
text = QtGui.QLineEdit(self)
text = QtWidgets.QLineEdit(self)
text.setText(str(self.settings[setting]))
text.textChanged.connect(lambda value=setting,\
var_name=setting: self.label_changed(value, var_name))
if self.bool_settings.has_key(setting):
chkbox = QtGui.QCheckBox(self)
if setting in self.bool_settings:
chkbox = QtWidgets.QCheckBox(self)
chkbox.setChecked(self.bool_settings[setting])
chkbox.stateChanged.connect(lambda value=setting,\
var_name=setting:\
......@@ -60,7 +61,7 @@ class NameListEditor(QtGui.QWidget):
grid.addWidget(chkbox, index, 0)
elif type(self.settings[setting]).__name__ == 'bool':
text = QtGui.QComboBox(self)
text = QtWidgets.QComboBox(self)
text.insertItem(0, 'True')
text.insertItem(1, 'False')
if self.settings[setting]:
......@@ -83,22 +84,22 @@ class NameListEditor(QtGui.QWidget):
client.setLayout(grid)
#scrollbars
scroll_area = QtGui.QScrollArea(self)
scroll_area = QtWidgets.QScrollArea(self)
#scroll_area.setHorizontalScrollBarPolicy(Qt.ScrollBarAlwaysOff)
scroll_area.setWidget(client)
#save cancel buttons
btn_widget = QtGui.QWidget(self)
hbox_layout = QtGui.QHBoxLayout(self)
btn_save = QtGui.QPushButton('Save')
btn_widget = QtWidgets.QWidget(self)
hbox_layout = QtWidgets.QHBoxLayout(self)
btn_save = QtWidgets.QPushButton('Save')
btn_save.clicked.connect(self._btn_save_callback)
self.btn_cancel = QtGui.QPushButton('Close')
self.btn_cancel = QtWidgets.QPushButton('Close')
self.btn_cancel.clicked.connect(self._btn_cancel_callback)
hbox_layout.addWidget(btn_save)
hbox_layout.addWidget(self.btn_cancel)
btn_widget.setLayout(hbox_layout)
box_layout = QtGui.QVBoxLayout(self)
box_layout = QtWidgets.QVBoxLayout(self)
box_layout.addWidget(scroll_area)
box_layout.addWidget(btn_widget)
btn_widget.setMaximumWidth(400)
......@@ -109,7 +110,7 @@ class NameListEditor(QtGui.QWidget):
def label_changed(self, value, name):
""" callback when the text is changed in the text box"""
self.new_settings[name] = unicode(value).encode('utf_8')
self.new_settings[name] = str(value).encode('utf_8')
def combo_index_changed(self, value, name):
""" callback when the True/False drop down for the settings which has boolean value
......@@ -153,7 +154,7 @@ class NameListEditor(QtGui.QWidget):
try:
self.mask_settings_update.emit(float(self.settings['mask_max_depth']), float(self.settings['mask_shelfbreak_dist']))
except KeyError:
print 'Set the mask setting mask_max_depth and mask_shelfbreak_dist'
print('Set the mask setting mask_max_depth and mask_shelfbreak_dist')
if self.bool_settings['mask_file']:
self.bathymetry_update.emit(self.settings['bathy'],self.settings['mask_file'])
......
pynemo/gui/nemo_ncml_generator.py
View file @ 6f50bc0c
......@@ -6,13 +6,13 @@ Created on 6 Aug 2015
import logging
import os
import xml.etree.ElementTree as ET
from PyQt4 import QtGui
from PyQt4 import QtCore
from PyQt4.QtCore import pyqtSlot
import nemo_ncml_tab_widget
from PyQt5 import QtGui, QtWidgets
from PyQt5 import QtCore
from PyQt5.QtCore import pyqtSlot
from . import nemo_ncml_tab_widget
from thredds_crawler.crawl import Crawl
class Ncml_generator(QtGui.QDialog):
class Ncml_generator(QtWidgets.QDialog):
'''
Gui editor to capture user input for the purpose of generating NCML representation of pynemo source datasets.
'''
......@@ -30,35 +30,35 @@ class Ncml_generator(QtGui.QDialog):
self.baseFile = os.path.join(testpath,'base.ncml')
else:
self.baseFile = basefile
print 'ncml baseFile : ', str(self.baseFile)
print('ncml baseFile : ', str(self.baseFile))
self.filename = None # store the output file pointer
self.initUI()
def initUI(self):
QtGui.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
QtWidgets.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
'''
vbox is the top container
'''
#the
vbox = QtGui.QVBoxLayout(self)
vbox = QtWidgets.QVBoxLayout(self)
vbox.setSpacing(10)
vbox.setContentsMargins(10, 10, 5, 5)
'''
top panel for output file
'''
top_outfile_label = QtGui.QLabel(unicode('Output filename').encode('utf-8'))
self.top_outfile_name = QtGui.QLineEdit() #location is pre-defined
self.top_outfile_name.setToolTip(unicode('Define output file').encode('utf-8'))
top_outfile_label = QtWidgets.QLabel('Output filename')
self.top_outfile_name = QtWidgets.QLineEdit() #location is pre-defined
self.top_outfile_name.setToolTip('Define output file')
self.top_outfile_name.returnPressed.connect(self.get_fname_input)
top_outfile_button = QtGui.QPushButton(unicode('Select file').encode('utf-8'))
top_outfile_button = QtWidgets.QPushButton('Select file')
top_outfile_button.clicked.connect(self.get_fname)
top_grpBox = QtGui.QGroupBox(unicode('Define output file').encode('utf-8'), None)
top_grid = QtGui.QGridLayout(top_grpBox)
top_grpBox = QtWidgets.QGroupBox('Define output file', None)
top_grid = QtWidgets.QGridLayout(top_grpBox)
top_grid.setVerticalSpacing(5)
top_grid.setHorizontalSpacing(10)
top_grid.addWidget(top_outfile_label, 1, 0)
......@@ -68,23 +68,23 @@ class Ncml_generator(QtGui.QDialog):
'''
middle panel for tab folder
'''
self.tabWidget = QtGui.QTabWidget()
self.tracer_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Tracer").encode('utf-8'))
self.tabWidget = QtWidgets.QTabWidget()
self.tracer_tab = nemo_ncml_tab_widget.Ncml_tab("Tracer")
self.tracer_tab.setEnabled(False)
self.dynamic_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Dynamics").encode('utf-8'))
self.dynamic_tab = nemo_ncml_tab_widget.Ncml_tab("Dynamics")
self.dynamic_tab.setEnabled(False)
self.ice_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Ice").encode('utf-8'))
self.ice_tab = nemo_ncml_tab_widget.Ncml_tab("Ice")
self.ice_tab.setEnabled(False)
self.ecosys_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Ecosystem").encode('utf-8'))
self.ecosys_tab = nemo_ncml_tab_widget.Ncml_tab("Ecosystem")
self.ecosys_tab.setEnabled(False)
self.grid_tab = nemo_ncml_tab_widget.Ncml_tab(unicode("Grid").encode('utf-8'))
self.grid_tab = nemo_ncml_tab_widget.Ncml_tab("Grid")
self.grid_tab.setEnabled(False)
self.tabWidget.addTab(self.tracer_tab, unicode("Tracer").encode('utf-8'))
self.tabWidget.addTab(self.dynamic_tab, unicode("Dynamics").encode('utf-8'))
self.tabWidget.addTab(self.ice_tab, unicode("Ice").encode('utf-8'))
self.tabWidget.addTab(self.ecosys_tab, unicode("Ecosystem").encode('utf-8')) # should be disabled
self.tabWidget.addTab(self.grid_tab, unicode("Grid").encode('utf-8')) # should be disabled
self.tabWidget.addTab(self.tracer_tab, "Tracer")
self.tabWidget.addTab(self.dynamic_tab, "Dynamics")
self.tabWidget.addTab(self.ice_tab, "Ice")
self.tabWidget.addTab(self.ecosys_tab, "Ecosystem") # should be disabled
self.tabWidget.addTab(self.grid_tab, "Grid") # should be disabled
self.tabWidget.setMovable(False)
# if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
......@@ -93,13 +93,13 @@ class Ncml_generator(QtGui.QDialog):
'''
button bar
'''
go_btn = QtGui.QPushButton(unicode('Generate').encode('utf-8'))
go_btn.setToolTip(unicode('Add all variable definitions before generating NcML file.').encode('utf-8'))
cancel_btn = QtGui.QPushButton(unicode('Cancel').encode('utf-8'))
enable_btn = QtGui.QPushButton(unicode('Enable Tab').encode('utf-8'))
go_btn = QtWidgets.QPushButton('Generate')
go_btn.setToolTip('Add all variable definitions before generating NcML file.')
cancel_btn = QtWidgets.QPushButton('Cancel')
enable_btn = QtWidgets.QPushButton('Enable Tab')
#layout button bar
btn_hBox = QtGui.QHBoxLayout(None)
btn_hBox.setMargin(5)
btn_hBox = QtWidgets.QHBoxLayout(None)
btn_hBox.setContentsMargins(5, 5, 5, 5)
btn_hBox.setSpacing(10)
btn_hBox.setAlignment(QtCore.Qt.AlignRight)
btn_hBox.addWidget(enable_btn)
......@@ -120,7 +120,7 @@ class Ncml_generator(QtGui.QDialog):
#self.setLayout(grp_box)
self.setWindowIcon(QtGui.QIcon('/Users/jdha/anaconda/lib/python2.7/site-packages/pynemo-0.2-py2.7.egg/pynemo/gui/nemo_icon.png')) #doesn't work
self.setWindowTitle(unicode("PyNEMO NcML Generator").encode('utf-8'))
self.setWindowTitle("PyNEMO NcML Generator")
self.resize(650,300)
#has to change the default focus to stop the output file QTextedit to trigger the widget in focus when enter is pressed. Not sure why this happens???
......@@ -137,7 +137,7 @@ class Ncml_generator(QtGui.QDialog):
# When you call getOpenFileName, a file picker dialog is created
# and if the user selects a file, it's path is returned, and if not
# (ie, the user cancels the operation) None is returned
fname = QtGui.QFileDialog.getSaveFileName(self, 'Select output file', '', selectedFilter='*.ncml')
fname = QtWidgets.QFileDialog.getSaveFileName(self, 'Select output file', '', selectedFilter='*.ncml')
if fname:
self.filename = fname #returns a QString
self.top_outfile_name.setText(str(fname))
......@@ -155,9 +155,9 @@ class Ncml_generator(QtGui.QDialog):
@pyqtSlot()
def enable_btn_update(self, enable_btn):
if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
enable_btn.setText(unicode('Disable Tab').encode('utf-8'))
enable_btn.setText('Disable Tab')
else:
enable_btn.setText(unicode('Enable Tab').encode('utf-8'))
enable_btn.setText('Enable Tab')
'''
call back to handle the generate button pressed
'''
......@@ -167,10 +167,10 @@ class Ncml_generator(QtGui.QDialog):
#validate output file
if self.tabWidget.widget(self.tabWidget.currentIndex()).isEnabled() is True:
self.tabWidget.widget(self.tabWidget.currentIndex()).setEnabled(False)
enable_btn.setText(unicode('Enable Tab').encode('utf-8'))
enable_btn.setText('Enable Tab')
else:
self.tabWidget.widget(self.tabWidget.currentIndex()).setEnabled(True)
enable_btn.setText(unicode('Disable Tab').encode('utf-8'))
enable_btn.setText('Disable Tab')
'''
call back to handle the generate button pressed
......@@ -180,14 +180,14 @@ class Ncml_generator(QtGui.QDialog):
#validate output file
if self.filename is None or self.filename == "":
if self.top_outfile_name.text() is None or self.top_outfile_name.text() == "":
QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('No output file specified!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'No output file specified!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
return
else:
self.filename = self.top_outfile_name.text()
if(os.path.exists(os.path.dirname(str(self.filename)))) == False:
#if os.path.dirname(os.path.dirname(os.path.exists(os.path.normpath(str(self.filename))))) == False:
QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('Invalid output directory! Cannot generate file!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'Invalid output directory! Cannot generate file!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
#print 'invalid target directory! Cannot generate.'
return
......@@ -201,7 +201,7 @@ class Ncml_generator(QtGui.QDialog):
self.tracer_tab.vosaline.src != "" :
tabsList.extend([self.tracer_tab.votemper, self.tracer_tab.vosaline])
else:
QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the tracer tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the tracer tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
if self.ice_tab.isEnabled() is True:
......@@ -210,7 +210,7 @@ class Ncml_generator(QtGui.QDialog):
self.ice_tab.isnowthi.src != "" :
tabsList.extend([self.ice_tab.iicethic, self.ice_tab.ileadfra, self.ice_tab.isnowthi])
else:
QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the ice tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the ice tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
if self.dynamic_tab.isEnabled() is True:
if self.dynamic_tab.vozocrtx.src != "" and \
......@@ -218,7 +218,7 @@ class Ncml_generator(QtGui.QDialog):
self.dynamic_tab.sossheig.src != "" :
tabsList.extend([self.dynamic_tab.vozocrtx, self.dynamic_tab.vomecrty, self.dynamic_tab.sossheig])
else:
QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the dynamics tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the dynamics tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
if self.grid_tab.isEnabled() is True:
if self.grid_tab.gdept.src != "" and \
......@@ -229,14 +229,14 @@ class Ncml_generator(QtGui.QDialog):
self.grid_tab.e3v.src != "" :
tabsList.extend([self.grid_tab.gdept, self.grid_tab.gdepw, self.grid_tab.mbathy, self.grid_tab.e3t, self.grid_tab.e3u, self.grid_tab.e3v])
else:
QtGui.QMessageBox.information(self, unicode('Something is wrong').encode('utf-8'), unicode('Not all the variables under the grid tab have been defined!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'Something is wrong', 'Not all the variables under the grid tab have been defined!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
try:
self.generateNcML(tabsList) #go ahead and do it
except:
raise
QtGui.QMessageBox.information(self, unicode('Success.').encode('utf-8'), unicode('NcML file generated.').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'Success.', 'NcML file generated.', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
'''
Function to generates the NcML text and write it to the user defined output file
......@@ -248,68 +248,68 @@ class Ncml_generator(QtGui.QDialog):
self.root = self.tree.getroot()
#create a netcdf element for each tab variable
for tab in tabsList:
netcdfE = ET.Element(ns+unicode('netcdf').encode('utf-8')) #src directory is converted to the correct format when added/
netcdfE = ET.Element(ns+'netcdf') #src directory is converted to the correct format when added/
if str(tab.src).startswith("http:") or str(tab.src).startswith("https:"):
#Its url so use thredds crawler to get the urls
urls = self.url_trawler(tab.src,str(tab.regex))
aggE = ET.Element(ns+unicode('aggregation').encode('utf-8'), name=unicode(str(tab.name)).encode('utf-8'), type=unicode('joinExisting').encode('utf-8'), dimName=unicode('time_counter').encode('utf-8')) #tab.name already encoded
aggE = ET.Element(ns+'aggregation', name=str(tab.name), type='joinExisting', dimName='time_counter') #tab.name already encoded
for nc_url in urls:
tcNetcdf = ET.Element(ns+unicode('netcdf').encode('utf-8'), location=unicode(str(nc_url)).encode('utf-8'))
tcNetcdf = ET.Element(ns+'netcdf', location=str(nc_url))
aggE.append(tcNetcdf)
netcdfE.append(aggE)
else:
scanE = ET.Element(ns+unicode('scan').encode('utf-8'), location=unicode(str(tab.src)).encode('utf-8'), regExp=unicode(str(tab.regex)).encode('utf-8'))
scanE = ET.Element(ns+'scan', location=str(tab.src), regExp=str(tab.regex))
if tab.subdirs == True:
scanE.set(unicode('subdirs').encode('utf-8'), unicode('true').encode('utf-8'))
aggE = ET.Element(ns+unicode('aggregation').encode('utf-8'), name=unicode(str(tab.name)).encode('utf-8'), type=unicode('joinExisting').encode('utf-8'), dimName=unicode('time_counter').encode('utf-8')) #tab.name already encoded
scanE.set('subdirs', 'true')
aggE = ET.Element(ns+'aggregation', name=str(tab.name), type='joinExisting', dimName='time_counter') #tab.name already encoded
aggE.append(scanE)
netcdfE.append(aggE)
self.root[0].append(netcdfE) #add the new netcdf element to the top aggregation
#deal with variable name change TODO put this into a loop?
if tab.old_name is not None and tab.old_name != "":
vname = unicode('variable').encode('utf-8')
vname = 'variable'
#v is None
if tab.name == unicode('temperature').encode('utf-8') and tab.old_name != unicode('votemper').encode('utf-8'):
if tab.name == 'temperature' and tab.old_name != 'votemper':
v = ET.Element(ns+vname, name='votemper', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('salinity').encode('utf-8') and tab.old_name != unicode('vosaline').encode('utf-8'):
elif tab.name == 'salinity' and tab.old_name != 'vosaline':
v = ET.Element(ns+vname, name='vosaline', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('ice_thickness').encode('utf-8') and tab.old_name != unicode('iicethic').encode('utf-8'):
elif tab.name == 'ice_thickness' and tab.old_name != 'iicethic':
v = ET.Element(ns+vname, name='iicethic', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('leads_fraction').encode('utf-8') and tab.old_name != unicode('ileadfra').encode('utf-8'):
elif tab.name == 'leads_fraction' and tab.old_name != 'ileadfra':
v = ET.Element(ns+vname, name='ileadfra', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('snow_thickness').encode('utf-8') and tab.old_name != unicode('isnowthi').encode('utf-8'):
elif tab.name == 'snow_thickness' and tab.old_name != 'isnowthi':
v = ET.Element(ns+vname, name='isnowthi', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('zonal_velocity').encode('utf-8') and tab.old_name != unicode('vozocrtx').encode('utf-8'):
elif tab.name == 'zonal_velocity' and tab.old_name != 'vozocrtx':
v = ET.Element(ns+vname, name='vozocrtx', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('meridian_velocity').encode('utf-8') and tab.old_name != unicode('vomecrty').encode('utf-8'):
elif tab.name == 'meridian_velocity' and tab.old_name != 'vomecrty':
v = ET.Element(ns+vname, name='vomecrty', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('sea_surface_height').encode('utf-8') and tab.old_name != unicode('sossheig').encode('utf-8'):
elif tab.name == 'sea_surface_height' and tab.old_name != 'sossheig':
v = ET.Element(ns+vname, name='sossheig', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('depth_at_t_points').encode('utf-8') and tab.old_name != unicode('gdept').encode('utf-8'):
elif tab.name == 'depth_at_t_points' and tab.old_name != 'gdept':
v = ET.Element(ns+vname, name='gdept', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('depth_at_w_points').encode('utf-8') and tab.old_name != unicode('gdepw').encode('utf-8'):
elif tab.name == 'depth_at_w_points' and tab.old_name != 'gdepw':
v = ET.Element(ns+vname, name='gdepw', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('number_of_wet_levels').encode('utf-8') and tab.old_name != unicode('mbathy').encode('utf-8'):
elif tab.name == 'number_of_wet_levels' and tab.old_name != 'mbathy':
v = ET.Element(ns+vname, name='mbathy', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('vertical_scale_factors_at_t_points').encode('utf-8') and tab.old_name != unicode('e3t').encode('utf-8'):
elif tab.name == 'vertical_scale_factors_at_t_points' and tab.old_name != 'e3t':
v = ET.Element(ns+vname, name='e3t', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('vertical_scale_factors_at_u_points').encode('utf-8') and tab.old_name != unicode('e3u').encode('utf-8'):
elif tab.name == 'vertical_scale_factors_at_u_points' and tab.old_name != 'e3u':
v = ET.Element(ns+vname, name='e3u', orgName = str(tab.old_name))
self.root.append(v)
elif tab.name == unicode('vertical_scale_factors_at_v_points').encode('utf-8') and tab.old_name != unicode('e3v').encode('utf-8'):
elif tab.name == 'vertical_scale_factors_at_v_points' and tab.old_name != 'e3v':
v = ET.Element(ns+vname, name='e3v', orgName = str(tab.old_name))
self.root.append(v)
......@@ -317,7 +317,8 @@ class Ncml_generator(QtGui.QDialog):
try:
self.indent(self.root, 0) #24Aug15 format the xml for pretty printing
self.tree.write(self.filename, encoding='utf-8')
except IOError as (errno, strerror):
except IOError as xxx_todo_changeme:
(errno, strerror) = xxx_todo_changeme.args
self.logger.error("I/O error({0}): {1}".format(errno, strerror))
except:
self.logger.error('Error generating ncml file')
......@@ -331,9 +332,9 @@ class Ncml_generator(QtGui.QDialog):
parser = ET.XMLParser(encoding="utf-8")
tree = ET.parse(self.baseFile, parser=parser)
return tree
except ET.ParseError, v:
except ET.ParseError as v:
row, column = v.position
print "error on row", row, "column", column, ":", v
print("error on row", row, "column", column, ":", v)
'''
Function to format xml. Based on code provided by http://effbot.org/zone/element-lib
......
pynemo/gui/nemo_ncml_tab_widget.py
View file @ 6f50bc0c
......@@ -5,11 +5,11 @@ Created on 2 Jul 2015
'''
import logging
import os
from PyQt4 import QtGui
from PyQt4 import QtCore
from PyQt4.QtCore import pyqtSlot
from PyQt5 import QtGui, QtWidgets
from PyQt5 import QtCore
from PyQt5.QtCore import pyqtSlot
class Ncml_tab(QtGui.QWidget):
class Ncml_tab(QtWidgets.QWidget):
'''
tab contents to define child aggregation
'''
......@@ -28,49 +28,49 @@ class Ncml_tab(QtGui.QWidget):
def initUI(self):
QtGui.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
self.varStackedWidget = QtGui.QStackedWidget()
QtWidgets.QToolTip.setFont(QtGui.QFont('SansSerif', 11))
self.varStackedWidget = QtWidgets.QStackedWidget()
#variable chooser combobox
combo_vars = []
if(self.var == unicode("Tracer").encode('utf-8')):
combo_vars = [unicode('temperature').encode('utf-8'),unicode('salinity').encode('utf-8')] #votemper, vosaline
self.votemper = ncml_variable(unicode('temperature').encode('utf-8'),'votemper')
self.vosaline = ncml_variable(unicode('salinity').encode('utf-8'),'vosaline')
if(self.var == "Tracer"):
combo_vars = ['temperature','salinity'] #votemper, vosaline
self.votemper = ncml_variable('temperature','votemper')
self.vosaline = ncml_variable('salinity','vosaline')
self.varStackedWidget.addWidget(self._addStackWidget("votemper"))
self.varStackedWidget.addWidget(self._addStackWidget("vosaline"))
#debug
# print 'Tracer has ' + str(self.varStackedWidget.count())
elif(self.var == unicode("Ice").encode('utf-8')):
combo_vars = [unicode('ice thickness').encode('utf-8'),unicode('leads fraction').encode('utf-8'),unicode('snow thickness').encode('utf-8')] #'iicethic,ileadfra,isnowthi
self.iicethic = ncml_variable(unicode('ice_thickness').encode('utf-8'),'iicethic')
self.ileadfra = ncml_variable(unicode('leads_fraction').encode('utf-8'),'ileadfra')
self.isnowthi = ncml_variable(unicode('snow_thickness').encode('utf-8'),'isnowthi')
elif(self.var == "Ice"):
combo_vars = ['ice thickness','leads fraction','snow thickness'] #'iicethic,ileadfra,isnowthi
self.iicethic = ncml_variable('ice_thickness','iicethic')
self.ileadfra = ncml_variable('leads_fraction','ileadfra')
self.isnowthi = ncml_variable('snow_thickness','isnowthi')
self.varStackedWidget.addWidget(self._addStackWidget("iicethic"))
self.varStackedWidget.addWidget(self._addStackWidget("ileadfra"))
self.varStackedWidget.addWidget(self._addStackWidget("isnowthi"))
# print 'Ice has ' + str(self.varStackedWidget.count())
elif(self.var == unicode("Dynamics").encode('utf-8')):
combo_vars = [unicode('zonal velocity').encode('utf-8'), unicode('meridian velocity').encode('utf-8'), unicode('sea surface height').encode('utf-8')] #vozocrtx, vomecrty, sossheig
self.vozocrtx = ncml_variable(unicode('zonal_velocity').encode('utf-8'),'vozocrtx')
self.vomecrty = ncml_variable(unicode('meridian_velocity').encode('utf-8'),'vomecrty')
self.sossheig = ncml_variable(unicode('sea_surface_height').encode('utf-8'),'sossheig')
elif(self.var == "Dynamics"):
combo_vars = ['zonal velocity', 'meridian velocity', 'sea surface height'] #vozocrtx, vomecrty, sossheig
self.vozocrtx = ncml_variable('zonal_velocity','vozocrtx')
self.vomecrty = ncml_variable('meridian_velocity','vomecrty')
self.sossheig = ncml_variable('sea_surface_height','sossheig')
self.varStackedWidget.addWidget(self._addStackWidget("vozocrtx"))
self.varStackedWidget.addWidget(self._addStackWidget("vomecrty"))
self.varStackedWidget.addWidget(self._addStackWidget("sossheig"))
# print 'Dynamics has ' + str(self.varStackedWidget.count())
elif(self.var == unicode("Grid").encode('utf-8')):
combo_vars = [unicode('depth at T points').encode('utf-8'),
unicode('depth at W points').encode('utf-8'),
unicode('number of wet levels').encode('utf-8'),
unicode('vertical scale factor at T points').encode('utf-8'),
unicode('vertical scale factor at U points').encode('utf-8'),
unicode('vertical scale factor at V points').encode('utf-8')] #gdept,gdepw,mbathy
self.gdept = ncml_variable(unicode('depth_at_t_points').encode('utf-8'),'gdept')
self.gdepw = ncml_variable(unicode('depth_at_w_points').encode('utf-8'),'gdepw')
self.mbathy = ncml_variable(unicode('number_of_wet_levels').encode('utf-8'),'mbathy')
self.e3t = ncml_variable(unicode('vertical_scale_factors_at_t_points').encode('utf-8'),'e3t')
self.e3u = ncml_variable(unicode('vertical_scale_factors_at_u_points').encode('utf-8'),'e3u')
self.e3v = ncml_variable(unicode('vertical_scale_factors_at_v_points').encode('utf-8'),'e3v')
elif(self.var == "Grid"):
combo_vars = ['depth at T points',
'depth at W points',
'number of wet levels',
'vertical scale factor at T points',
'vertical scale factor at U points',
'vertical scale factor at V points'] #gdept,gdepw,mbathy
self.gdept = ncml_variable('depth_at_t_points','gdept')
self.gdepw = ncml_variable('depth_at_w_points','gdepw')
self.mbathy = ncml_variable('number_of_wet_levels','mbathy')
self.e3t = ncml_variable('vertical_scale_factors_at_t_points','e3t')
self.e3u = ncml_variable('vertical_scale_factors_at_u_points','e3u')
self.e3v = ncml_variable('vertical_scale_factors_at_v_points','e3v')
self.varStackedWidget.addWidget(self._addStackWidget("gdept"))
self.varStackedWidget.addWidget(self._addStackWidget("gdepw"))
self.varStackedWidget.addWidget(self._addStackWidget("mbathy"))
......@@ -82,7 +82,7 @@ class Ncml_tab(QtGui.QWidget):
vars = ['nitrate','silicate'] #nitrate, silicate
self.varStackedWidget.setCurrentIndex(0) #we rely on the stacked tab index to be the same as the combo box
#combo box
self.var_combo = QtGui.QComboBox()
self.var_combo = QtWidgets.QComboBox()
self.var_combo.addItems(combo_vars)
self.var_combo.setEditable(False)
self.var_combo.setCurrentIndex(0)
......@@ -90,20 +90,20 @@ class Ncml_tab(QtGui.QWidget):
self.var_combo.currentIndexChanged.connect(lambda var_name = self.var : self.src_combo_changed(var_name))
self.var_combo.currentIndexChanged.connect(self.setWidgetStack)
#label
var_label = QtGui.QLabel(unicode('Variable').encode('utf-8'))
var_label = QtWidgets.QLabel('Variable')
#set layout
stacked_hBox = QtGui.QHBoxLayout()
stacked_hBox.setMargin(5)
stacked_hBox = QtWidgets.QHBoxLayout()
stacked_hBox.setContentsMargins(5, 5, 5, 5)
stacked_hBox.setSpacing(50) # spacing between items
stacked_hBox.setAlignment(QtCore.Qt.AlignLeft)
stacked_hBox.addWidget(var_label)
stacked_hBox.addWidget(self.var_combo)
#
vBoxLayout = QtGui.QVBoxLayout()
vBoxLayout = QtWidgets.QVBoxLayout()
vBoxLayout.addLayout(stacked_hBox)
vBoxLayout.addWidget(self.varStackedWidget)
#
grp_box = QtGui.QGroupBox(None)
grp_box = QtWidgets.QGroupBox(None)
grp_box.setLayout(vBoxLayout)
'''
......@@ -115,24 +115,24 @@ class Ncml_tab(QtGui.QWidget):
button bar
'''
# reset button
reset_btn = QtGui.QPushButton(unicode('Reset').encode('utf-8'))
reset_btn.setToolTip(unicode('Reset fields to previously saved values').encode('utf-8'))
add_btn = QtGui.QPushButton(unicode('Add').encode('utf-8'))
reset_btn = QtWidgets.QPushButton('Reset')
reset_btn.setToolTip('Reset fields to previously saved values')
add_btn = QtWidgets.QPushButton('Add')
add_btn.setDefault(True)
add_btn.setToolTip(unicode('Add the current definition to the NcML').encode('utf-8'))
add_btn.setToolTip('Add the current definition to the NcML')
#connect up with events
reset_btn.clicked.connect(self.reset_tab)
add_btn.clicked.connect(self.add_tab)
btn_hBox = QtGui.QHBoxLayout(None)
btn_hBox.setMargin(5)
btn_hBox = QtWidgets.QHBoxLayout(None)
btn_hBox.setContentsMargins(5, 5, 5, 5)
btn_hBox.setSpacing(10)
btn_hBox.setAlignment(QtCore.Qt.AlignCenter)
btn_hBox.addWidget(reset_btn)
btn_hBox.addWidget(add_btn)
#build the contents
vbox = QtGui.QVBoxLayout(self)
vbox = QtWidgets.QVBoxLayout(self)
vbox.setSpacing(10)
vbox.setContentsMargins(10, 10, 5, 5)
vbox.addWidget(grp_box)
......@@ -141,30 +141,30 @@ class Ncml_tab(QtGui.QWidget):
create the stacked widget for each nemo variable
'''
def _addStackWidget(self, old_name=""):
self.varWidget = QtGui.QWidget()
self.varWidget = QtWidgets.QWidget()
#self.varWidget.setObjectName(objName)
varLayout = QtGui.QGridLayout()
varLayout = QtWidgets.QGridLayout()
varLayout.setSpacing(20)
#labels
src_label = QtGui.QLabel(unicode('Source directory*').encode('utf-8'))
cbox_label = QtGui.QLabel(unicode('Includes subdirs').encode('utf-8'))
regex_label = QtGui.QLabel(unicode('Regular expression').encode('utf-8'))
old_name_label = QtGui.QLabel(unicode('Existing variable name*').encode('utf-8'))
src_label = QtWidgets.QLabel('Source directory*')
cbox_label = QtWidgets.QLabel('Includes subdirs')
regex_label = QtWidgets.QLabel('Regular expression')
old_name_label = QtWidgets.QLabel('Existing variable name*')
#input textboxs
self.varWidget.src_tedit = QtGui.QLineEdit() # input widgets need to be attached to the stacked widget itself
self.varWidget.src_tedit.setToolTip(unicode('either remote OPeNDAP server or local file absolute path').encode('utf-8'))
self.varWidget.src_tedit = QtWidgets.QLineEdit() # input widgets need to be attached to the stacked widget itself
self.varWidget.src_tedit.setToolTip('either remote OPeNDAP server or local file absolute path')
self.varWidget.src_tedit.returnPressed.connect(self.src_tedit_edited)
self.varWidget.cbox = QtGui.QCheckBox()
self.varWidget.cbox = QtWidgets.QCheckBox()
self.varWidget.cbox.setCheckable(True)
self.varWidget.cbox.setChecked(False)
self.varWidget.cbox.setToolTip(unicode('includes subdirectories').encode('utf-8'))
self.varWidget.regex_tedit = QtGui.QLineEdit()
self.varWidget.regex_tedit.setToolTip(unicode('see http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp').encode('utf-8'))
self.varWidget.old_name_tedit = QtGui.QLineEdit()
self.varWidget.old_name_tedit.setToolTip(unicode('variable name in data file').encode('utf-8'))
self.varWidget.cbox.setToolTip('includes subdirectories')
self.varWidget.regex_tedit = QtWidgets.QLineEdit()
self.varWidget.regex_tedit.setToolTip('see http://www.unidata.ucar.edu/software/thredds/current/netcdf-java/ncml/AnnotatedSchema4.html#regexp')
self.varWidget.old_name_tedit = QtWidgets.QLineEdit()
self.varWidget.old_name_tedit.setToolTip('variable name in data file')
self.varWidget.old_name_tedit.setText(old_name)
varLayout.addWidget(src_label, 1, 0, 1, 1)
......@@ -201,10 +201,10 @@ class Ncml_tab(QtGui.QWidget):
#validate the input now
if not str(src_tedit_input).startswith('http'):
if not os.path.isabs(src_tedit_input): #assumes local file
QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory must be an absolute path!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory must be an absolute path!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
self.varStackedWidget.currentWidget().src_tedit.clear()
if not os.path.exists(src_tedit_input) :
QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory does not exist!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory does not exist!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
self.varStackedWidget.currentWidget().src_tedit.clear()
'''
reset button pushed callback. The widgets are reset to default values
......@@ -213,34 +213,34 @@ class Ncml_tab(QtGui.QWidget):
def reset_tab(self):
#current screen value is not saved until the add button is pressed
#reset only reset the screen values, not the cached values
if self.var_combo.currentText() == unicode("temperature").encode('utf-8'):
if self.var_combo.currentText() == "temperature":
# print 'reset button is pushed, temperature ....'
self.resetValues(self.votemper)
elif self.var_combo.currentText() == unicode("salinity").encode('utf-8'):
elif self.var_combo.currentText() == "salinity":
self.resetValues(self.vosaline)
elif self.var_combo.currentText() == unicode("ice thickness").encode('utf-8'):
elif self.var_combo.currentText() == "ice thickness":
self.resetValues(self.iicethic)
elif self.var_combo.currentText() == unicode("leads fraction").encode('utf-8'):
elif self.var_combo.currentText() == "leads fraction":
self.resetValues(self.ileadfra)
elif self.var_combo.currentText() == unicode("snow thickness").encode('utf-8'):
elif self.var_combo.currentText() == "snow thickness":
self.resetValues(self.isnowthi)
elif self.var_combo.currentText() == unicode("zonal velocity").encode('utf-8'):
elif self.var_combo.currentText() == "zonal velocity":
self.resetValues(self.vozocrtx)
elif self.var_combo.currentText() == unicode("meridian velocity").encode('utf-8'):
elif self.var_combo.currentText() == "meridian velocity":
self.resetValues(self.vomecrty)
elif self.var_combo.currentText() == unicode("sea surface height").encode('utf-8'):
self.resetValues(self.sossheig)
elif self.var_combo.currentText() == unicode("depth at T points").encode('utf-8'):
elif self.var_combo.currentText() == "sea surface height":
self.resetValues(self.sossheig)
elif self.var_combo.currentText() == "depth at T points":
self.resetValues(self.gdept)
elif self.var_combo.currentText() == unicode("depth at W points").encode('utf-8'):
elif self.var_combo.currentText() == "depth at W points":
self.resetValues(self.gdepw)
elif self.var_combo.currentText() == unicode("number of wet levels").encode('utf-8'):
elif self.var_combo.currentText() == "number of wet levels":
self.resetValues(self.mbathy)
elif self.var_combo.currentText() == unicode("vertical scale factor at T points").encode('utf-8'):
elif self.var_combo.currentText() == "vertical scale factor at T points":
self.resetValues(self.e3t)
elif self.var_combo.currentText() == unicode("vertical scale factor at U points").encode('utf-8'):
elif self.var_combo.currentText() == "vertical scale factor at U points":
self.resetValues(self.e3u)
elif self.var_combo.currentText() == unicode("vertical scale factor at V points").encode('utf-8'):
elif self.var_combo.currentText() == "vertical scale factor at V points":
self.resetValues(self.e3v)
'''
......@@ -270,7 +270,7 @@ class Ncml_tab(QtGui.QWidget):
#first validate the src tab is not null
if(self.varStackedWidget.currentWidget().src_tedit.text() is None or self.varStackedWidget.currentWidget().src_tedit.text() == '' or
self.varStackedWidget.currentWidget().old_name_tedit.text() is None or self.varStackedWidget.currentWidget().old_name_tedit.text() == ''):
QtGui.QMessageBox.critical(self, unicode('Something is wrong').encode('utf-8'), unicode('source directory and existing variable name cannot be blank!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.critical(self, 'Something is wrong', 'source directory and existing variable name cannot be blank!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
'''
if not str(target).startsWith(unicode('http').encode('utf-8')):
......@@ -283,10 +283,10 @@ class Ncml_tab(QtGui.QWidget):
# be in the same directory.
if(self.var == unicode("Tracer").encode('utf-8')):
if (self.var_combo.currentText() == unicode("temperature").encode('utf-8')):
if(self.var == "Tracer"):
if (self.var_combo.currentText() == "temperature"):
if(self._sameValues(self.votemper)):
QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.votemper.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.votemper.old_name = self.varStackedWidget.currentWidget().old_name_tedit.text()
......@@ -297,7 +297,7 @@ class Ncml_tab(QtGui.QWidget):
self.votemper.regex = '' #blank it over
else: # can only be salinity
if(self._sameValues(self.vosaline)):
QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.vosaline.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.vosaline.old_name = self.varStackedWidget.currentWidget().old_name_tedit.text()
......@@ -312,10 +312,10 @@ class Ncml_tab(QtGui.QWidget):
if self.vosaline.src == '':
self.vosaline.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.varStackedWidget.widget(1).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
elif(self.var == unicode('Ice').encode('utf-8')): #iicethic,ileadfra,isnowthi
if (self.var_combo.currentText() == unicode("ice thickness").encode('utf-8')):
elif(self.var == 'Ice'): #iicethic,ileadfra,isnowthi
if (self.var_combo.currentText() == "ice thickness"):
if(self._sameValues(self.iicethic)):
QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.iicethic.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.iicethic.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -324,9 +324,9 @@ class Ncml_tab(QtGui.QWidget):
self.iicethic.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.iicethic.regex = ''
elif(self.var_combo.currentText() == unicode("leads fraction").encode('utf-8')):
elif(self.var_combo.currentText() == "leads fraction"):
if(self._sameValues(self.ileadfra)):
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.ileadfra.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.ileadfra.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -337,7 +337,7 @@ class Ncml_tab(QtGui.QWidget):
self.ileadfra.regex = ''
else:
if(self._sameValues(self.isnowthi)): #snow thickness
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.isnowthi.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.isnowthi.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -355,10 +355,10 @@ class Ncml_tab(QtGui.QWidget):
if self.isnowthi.src == '':
self.isnowthi.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.varStackedWidget.widget(2).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
elif(self.var == unicode("Dynamics").encode('utf-8')):
if (self.var_combo.currentText() == unicode("zonal velocity").encode('utf-8')):
elif(self.var == "Dynamics"):
if (self.var_combo.currentText() == "zonal velocity"):
if(self._sameValues(self.vozocrtx)):
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.vozocrtx.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.vozocrtx.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -367,9 +367,9 @@ class Ncml_tab(QtGui.QWidget):
self.vozocrtx.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.vozocrtx.regex = ''
elif(self.var_combo.currentText() == unicode('meridian velocity').encode('utf-8')):
elif(self.var_combo.currentText() == 'meridian velocity'):
if(self._sameValues(self.vomecrty)):
QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.vomecrty.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.vomecrty.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -378,9 +378,9 @@ class Ncml_tab(QtGui.QWidget):
self.vomecrty.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.vomecrty.regex = ''
elif(self.var_combo.currentText() == unicode('sea surface height').encode('utf-8')):
elif(self.var_combo.currentText() == 'sea surface height'):
if(self._sameValues(self.sossheig)): #sea surface height
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.sossheig.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.sossheig.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -398,10 +398,10 @@ class Ncml_tab(QtGui.QWidget):
if self.sossheig.src == '':
self.sossheig.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.varStackedWidget.widget(2).src_tedit.setText(self.varStackedWidget.currentWidget().src_tedit.text())
elif(self.var == unicode("Grid").encode('utf-8')):
if (self.var_combo.currentText() == unicode("depth at T points").encode('utf-8')):
elif(self.var == "Grid"):
if (self.var_combo.currentText() == "depth at T points"):
if(self._sameValues(self.gdept)):
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.gdept.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.gdept.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -410,9 +410,9 @@ class Ncml_tab(QtGui.QWidget):
self.gdept.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.gdept.regex = ''
elif(self.var_combo.currentText() == unicode('depth at W points').encode('utf-8')):
elif(self.var_combo.currentText() == 'depth at W points'):
if(self._sameValues(self.gdepw)):
QtGui.QMessageBox.information(self, 'For information', 'No changes have been made!', QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.gdepw.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.gdepw.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -421,9 +421,9 @@ class Ncml_tab(QtGui.QWidget):
self.gdepw.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.gdepw.regex = ''
elif(self.var_combo.currentText() == unicode('number of wet levels').encode('utf-8')):
elif(self.var_combo.currentText() == 'number of wet levels'):
if(self._sameValues(self.mbathy)): #sea surface height
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.mbathy.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.mbathy.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -432,9 +432,9 @@ class Ncml_tab(QtGui.QWidget):
self.mbathy.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.mbathy.regex = ''
elif(self.var_combo.currentText() == unicode('vertical scale factor at T points').encode('utf-8')):
elif(self.var_combo.currentText() == 'vertical scale factor at T points'):
if(self._sameValues(self.e3t)): #sea surface height
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.e3t.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.e3t.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -443,9 +443,9 @@ class Ncml_tab(QtGui.QWidget):
self.e3t.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.e3t.regex = ''
elif(self.var_combo.currentText() == unicode('vertical scale factor at U points').encode('utf-8')):
elif(self.var_combo.currentText() == 'vertical scale factor at U points'):
if(self._sameValues(self.e3u)): #sea surface height
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.e3u.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.e3u.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -454,9 +454,9 @@ class Ncml_tab(QtGui.QWidget):
self.e3u.regex = self.varStackedWidget.currentWidget().regex_tedit.text()
else:
self.e3u.regex = ''
elif(self.var_combo.currentText() == unicode('vertical scale factor at V points').encode('utf-8')):
elif(self.var_combo.currentText() == 'vertical scale factor at V points'):
if(self._sameValues(self.e3v)): #sea surface height
QtGui.QMessageBox.information(self, unicode('For information').encode('utf-8'), unicode('No changes have been made!').encode('utf-8'), QtGui.QMessageBox.Ok, QtGui.QMessageBox.Ok)
QtWidgets.QMessageBox.information(self, 'For information', 'No changes have been made!', QtWidgets.QMessageBox.Ok, QtWidgets.QMessageBox.Ok)
else:
self.e3v.src = self._convertSrc(self.varStackedWidget.currentWidget().src_tedit.text())
self.e3v.subdirs = self.varStackedWidget.currentWidget().cbox.isChecked()
......@@ -497,10 +497,10 @@ class Ncml_tab(QtGui.QWidget):
elif fpath.startswith('file:/'):
temp = os.path.normpath(fpath[6:])
# print 'normal path : ', temp
target = unicode('file:/' + str(os.path.abspath(temp)).replace("\\", "/")).encode('utf-8')
target = str('file:/' + str(os.path.abspath(temp)).replace("\\", "/")).encode('utf-8')
else: #should be local file but not prefixed by file:/ we still check for absolute path
# print 'normal path : ', os.path.normpath(fpath)
target = unicode('file:/' + str(os.path.abspath(fpath)).replace("\\", "/")).encode('utf-8')
target = str('file:/' + str(os.path.abspath(fpath)).replace("\\", "/")).encode('utf-8')
# if not str(target).endswith('/'):
# target = target + '/'
......
pynemo/gui/selection_editor.py
View file @ 6f50bc0c
......@@ -9,7 +9,7 @@ import numpy as np
from matplotlib.lines import Line2D
from matplotlib.patches import Polygon
from matplotlib.artist import Artist
from matplotlib.mlab import dist_point_to_segment
from pynemo.utils.nemo_bdy_lib import dist_point_to_segment
from matplotlib.widgets import RectangleSelector
......@@ -58,12 +58,12 @@ class PolygonEditor(object):
self.reset_line()
self.reset_polygon()
elif self.xy_values.shape[0] <= 2: # point or line for 1 or 2 points
xval, yval = zip(*self.xy_values)
xval, yval = list(zip(*self.xy_values))
if self.line == None:
self.line = Line2D(xval, yval, marker='o', markerfacecolor='r', animated=True)
self.axis.add_line(self.line)
else:
self.line.set_data(zip(*self.xy_values))
self.line.set_data(list(zip(*self.xy_values)))
self.reset_polygon()
else: # more than 2 points if polygon is not created then creates one and draws
if self.polygon == None:
......@@ -72,7 +72,7 @@ class PolygonEditor(object):
self.axis.add_patch(self.polygon)
else:
self.polygon.xy = self.xy_values
self.line.set_data(zip(*self.xy_values))
self.line.set_data(list(zip(*self.xy_values)))
self.draw_callback(None)
self.canvas.draw()
......
pynemo/nemo_bdy_extr_tm3.py
View file @ 6f50bc0c
......@@ -38,12 +38,12 @@ import numpy as np
import scipy.spatial as sp
from calendar import monthrange, isleap
from scipy.interpolate import interp1d
from netcdftime import datetime, utime
from cftime import datetime, utime
from pynemo import nemo_bdy_ncgen as ncgen
from pynemo import nemo_bdy_ncpop as ncpop
# Local Imports
import nemo_bdy_grid_angle as ga
from . import nemo_bdy_grid_angle as ga
from pynemo.reader.factory import GetFile
from pynemo.utils.nemo_bdy_lib import rot_rep, sub2ind
......@@ -233,12 +233,12 @@ class Extract:
# Ann Query substitute
source_tree = None
try:
source_tree = sp.cKDTree(zip(SC.lon.ravel(order='F'),
SC.lat.ravel(order='F')), balanced_tree=False,compact_nodes=False)
source_tree = sp.cKDTree(list(zip(SC.lon.ravel(order='F'),
SC.lat.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
except TypeError: #added this fix to make it compatible with scipy 0.16.0
source_tree = sp.cKDTree(zip(SC.lon.ravel(order='F'),
SC.lat.ravel(order='F')))
dst_pts = zip(dst_lon[:].ravel(order='F'), dst_lat[:].ravel(order='F'))
source_tree = sp.cKDTree(list(zip(SC.lon.ravel(order='F'),
SC.lat.ravel(order='F'))))
dst_pts = list(zip(dst_lon[:].ravel(order='F'), dst_lat[:].ravel(order='F')))
nn_dist, nn_id = source_tree.query(dst_pts, k=1)
# Find surrounding points
......@@ -280,8 +280,8 @@ class Extract:
ind[p, :] = ind[p, dist_ind[p, :]]
if self.key_vec:
self.gcos = self.gcos.flatten(1)[ind].reshape(ind.shape, order='F')
self.gsin = self.gsin.flatten(1)[ind].reshape(ind.shape, order='F')
self.gcos = self.gcos.flatten('F')[ind].reshape(ind.shape, order='F')
self.gsin = self.gsin.flatten('F')[ind].reshape(ind.shape, order='F')
sc_ind = {}
sc_ind['ind'] = ind
......@@ -301,14 +301,14 @@ class Extract:
tmp_lat[r_id] = -9999
source_tree = None
try:
source_tree = sp.cKDTree(zip(tmp_lon.ravel(order='F'),
tmp_lat.ravel(order='F')), balanced_tree=False,compact_nodes=False)
source_tree = sp.cKDTree(list(zip(tmp_lon.ravel(order='F'),
tmp_lat.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
except TypeError: #fix for scipy 0.16.0
source_tree = sp.cKDTree(zip(tmp_lon.ravel(order='F'),
tmp_lat.ravel(order='F')))
source_tree = sp.cKDTree(list(zip(tmp_lon.ravel(order='F'),
tmp_lat.ravel(order='F'))))
dst_pts = zip(dst_lon[rr_id].ravel(order='F'),
dst_lat[rr_id].ravel(order='F'))
dst_pts = list(zip(dst_lon[rr_id].ravel(order='F'),
dst_lat[rr_id].ravel(order='F')))
junk, an_id = source_tree.query(dst_pts, k=3,
distance_upper_bound=fr)
id_121[rr_id, :] = an_id
......@@ -347,11 +347,11 @@ class Extract:
z_ind = np.zeros((num_bdy * dst_len_z, 2), dtype=np.int64)
source_tree = None
try:
source_tree = sp.cKDTree(zip(sc_z.ravel(order='F')), balanced_tree=False,compact_nodes=False)
source_tree = sp.cKDTree(list(zip(sc_z.ravel(order='F'))), balanced_tree=False,compact_nodes=False)
except TypeError: #fix for scipy 0.16.0
source_tree = sp.cKDTree(zip(sc_z.ravel(order='F')))
source_tree = sp.cKDTree(list(zip(sc_z.ravel(order='F'))))
junk, nn_id = source_tree.query(zip(dst_dep_rv), k=1)
junk, nn_id = source_tree.query(list(zip(dst_dep_rv)), k=1)
# WORKAROUND: the tree query returns out of range val when
# dst_dep point is NaN, causing ref problems later.
......@@ -453,7 +453,7 @@ class Extract:
# Get first and last date within range, init to cover entire range
first_date = 0
last_date = len(sc_time.time_counter) - 1
rev_seq = range(len(sc_time.time_counter))
rev_seq = list(range(len(sc_time.time_counter)))
rev_seq.reverse()
for date in rev_seq:
if src_date_seconds[date] < dst_start:
......@@ -571,11 +571,11 @@ class Extract:
for dep in range(sc_z_len):
tmp_arr = [None, None]
# Consider squeezing
tmp_arr[0] = sc_array[0][0,dep,:,:].flatten(1) #[:,:,dep]
tmp_arr[0] = sc_array[0][0,dep,:,:].flatten('F') #[:,:,dep]
if not self.key_vec:
sc_bdy[vn, dep, :, :] = self._flat_ref(tmp_arr[0], ind)
else:
tmp_arr[1] = sc_array[1][0,dep,:,:].flatten(1) #[:,:,dep]
tmp_arr[1] = sc_array[1][0,dep,:,:].flatten('F') #[:,:,dep]
# Include in the collapse the rotation from the
# grid to real zonal direction, ie ij -> e
sc_bdy[vn, dep, :] = (tmp_arr[0][ind[:]] * self.gcos -
......@@ -669,11 +669,11 @@ class Extract:
# Apply 1-2-1 filter along bdy pts using NN ind self.id_121
if self.first:
tmp_valid = np.invert(np.isnan(
dst_bdy.flatten(1)[self.id_121]))
dst_bdy.flatten('F')[self.id_121]))
# Finished first run operations
self.first = False
dst_bdy = (np.nansum(dst_bdy.flatten(1)[self.id_121] *
dst_bdy = (np.nansum(dst_bdy.flatten('F')[self.id_121] *
self.tmp_filt, 2) / np.sum(self.tmp_filt *
tmp_valid, 2))
# Set land pts to zero
......@@ -688,7 +688,7 @@ class Extract:
# If we have depth dimension
if not self.isslab:
# If all else fails fill down using deepest pt
dst_bdy = dst_bdy.flatten(1)
dst_bdy = dst_bdy.flatten('F')
dst_bdy += ((dst_bdy == 0) *
dst_bdy[data_ind].repeat(sc_z_len))
# Weighted averaged on new vertical grid
......@@ -732,7 +732,7 @@ class Extract:
alpha -- input array
beta -- index array
"""
return alpha.flatten(1)[beta.flatten(1)].reshape(
return alpha.flatten('F')[beta.flatten('F')].reshape(
beta.shape, order='F')
# Convert numeric date from source to dest
......@@ -752,7 +752,7 @@ class Extract:
"""
vals = {'gregorian': 365. + isleap(year), 'noleap':
365., '360_day': 360.}
if source not in vals.keys():
if source not in list(vals.keys()):
raise ValueError('Unknown source calendar type: %s' %source)
# Get month length
if dest == '360_day':
......
pynemo/nemo_bdy_gen_c.py
View file @ 6f50bc0c
......@@ -13,7 +13,7 @@ import numpy as np
import logging
#Local Imports
from utils.nemo_bdy_lib import sub2ind
from .utils.nemo_bdy_lib import sub2ind
class Boundary:
# Bearings for overlays
......@@ -102,8 +102,8 @@ class Boundary:
bdy_i = np.transpose(bdy_i, (1, 2, 0))
bdy_i = np.reshape(bdy_i,
(bdy_i.shape[0],bdy_i.shape[1]*bdy_i.shape[2]))
bdy_r = bdy_r.flatten(1)
bdy_r = bdy_r.flatten('F')
## Remove duplicate and open sea points ##
bdy_i, bdy_r = self._remove_duplicate_points(bdy_i, bdy_r)
......@@ -210,11 +210,11 @@ class Boundary:
t -- input 2D array
"""
sh = np.shape(t)
if (len(sh)> 2) or (sh[0] ==0) or (sh[1] == 0):
print 'Warning: Shape of expected 2D array:', sh
if (len(sh)> 2) or (sh[0] ==0) or (sh[1] == 0):
print('Warning: Shape of expected 2D array:', sh)
tlist = t.tolist()
sortt = []
indx = zip(*sorted([(val, i) for i,val in enumerate(tlist)]))[1]
indx = list(zip(*sorted([(val, i) for i,val in enumerate(tlist)])))[1]
indx = np.array(indx)
for i in indx:
sortt.append(tlist[i])
......@@ -224,7 +224,7 @@ class Boundary:
indx[i] = -1
# all the rows are identical, set the first as the unique row
if sortt[0] == sortt[-1]:
indx[0] = 0
indx[0] = 0
return indx[indx != -1]
pynemo/nemo_bdy_grid_angle.py
View file @ 6f50bc0c
......@@ -13,7 +13,7 @@
# cd_type: define the nature of pt2d grid points
import numpy as np
from reader.factory import GetFile
from .reader.factory import GetFile
import logging
# pylint: disable=E1101
......
pynemo/nemo_bdy_ncpop.py
View file @ 6f50bc0c
......@@ -23,13 +23,13 @@ def write_data_to_file(filename, variable_name, data):
if variable_name in three_dim_variables:
if len(count) == 3:
count += (1L, )
count += (1, )
ncid.variables[variable_name][:, :, :, :] = np.reshape(data, count)[:, :, :, :]
elif variable_name in two_dim_variables:
if len(count) == 2:
count += (1L, )
count += (1, )
elif len(count) == 1:
count += (1L, 1L, )
count += (1, 1, )
ncid.variables[variable_name][:, :, :] = np.reshape(data, count)[:, :, :]
elif variable_name == 'time_counter':
ncid.variables[variable_name][:] = data[:]
......
pynemo/nemo_bdy_setup.py
View file @ 6f50bc0c
......@@ -204,11 +204,11 @@ def _get_val(vars_dictionary, bool_vars_dictionary, line):
if name_prefix == 'ln':
if value.find('true') is not -1:
if vars_dictionary.has_key(name) != True:
if (name in vars_dictionary) != True:
vars_dictionary[name] = True
bool_vars_dictionary[name] = True
elif value.find('false') is not -1:
if vars_dictionary.has_key(name) != True:
if (name in vars_dictionary) != True:
vars_dictionary[name] = False
bool_vars_dictionary[name] = False
else:
......
pynemo/nemo_bdy_src_time.py
View file @ 6f50bc0c
......@@ -29,7 +29,7 @@ class SourceTime:
dir_list.sort()
return filter(None, dir_list)
return [_f for _f in dir_list if _f]
# Returns list of dicts of date/time info
# I assume there is only one date per file
......
pynemo/nemo_bdy_zgrv2.py
View file @ 6f50bc0c
......@@ -14,12 +14,12 @@ Initialise with bdy t, u and v grid attributes (Grid.bdy_i)
and settings dictionary
"""
from reader.factory import GetFile
from .reader.factory import GetFile
import numpy as np
import logging
from utils.nemo_bdy_lib import sub2ind
from utils.e3_to_depth import e3_to_depth
from .utils.nemo_bdy_lib import sub2ind
from .utils.e3_to_depth import e3_to_depth
# pylint: disable=E1101
# Query name
class Depth:
......@@ -52,6 +52,7 @@ class Depth:
# Check inputs
# FIX ME? Errors for wrong obj arg len. probably better to work around
print(settings)
if settings['sco']:
# hc = ... FIX ME??
# Depth of water column at t-point
......@@ -68,7 +69,7 @@ class Depth:
v_ind = sub2ind(mbathy.shape, bdy_v[:,0], bdy_v[:,1])
v_ind2 = sub2ind(mbathy.shape, bdy_v[:,0], bdy_v[:,1] + 1)
[tmp_zt, tmp_zw] = e3_to_depth(np.squeeze(nc['e3t'][:,:,:,:]), np.squeeze(nc['e3w'][:,:,:,:]), nz)
[tmp_zt, tmp_zw] = e3_to_depth(np.squeeze(nc['e3t'][:,:,:,:]), np.squeeze(nc['e3w'][:,:,:,:]), nz)
# This is very slow
self.logger.debug( 'starting nc reads loop' )
for k in range(nz):
......@@ -95,12 +96,12 @@ class Depth:
# Set u and v grid point depths
zshapes = {}
for p in self.zpoints.keys():
for p in list(self.zpoints.keys()):
zshapes[p] = self.zpoints[p].shape
wshapes = []
wshapes.append(wrk1.shape)
wshapes.append(wrk2.shape)
wrk1, wrk2 = wrk1.flatten(1), wrk2.flatten(1)
wrk1, wrk2 = wrk1.flatten('F'), wrk2.flatten('F')
self.zpoints['t'][k,:] = wrk1[t_ind]
self.zpoints['wt'][k,:] = wrk2[t_ind]
......@@ -111,7 +112,7 @@ class Depth:
self.zpoints['v'][k,:] = 0.5 * (wrk1[v_ind] + wrk1[v_ind2])
self.zpoints['wv'][k,:] = 0.5 * (wrk2[v_ind] + wrk2[v_ind2])
for p in self.zpoints.keys():
for p in list(self.zpoints.keys()):
self.zpoints[p] = self.zpoints[p].reshape(zshapes[p])
self.logger.debug( 'Done loop, zpoints: %s ', self.zpoints['t'].shape)
......
pynemo/nemo_bogadons_gauntlet.py deleted 100644 → 0
View file @ b1ee0b2f
#
# The loop from nemo_bdy_extr_tm3
#
#
#
from calendar import monthrange
from datetime import datetime
from netCDF4 import Dataset, netcdftime
class Enter:
def __init__(self, settings, sc_time, dir_list, dst_cal_type, year, month):
var_nam = ['votemper', 'vosaline']
sc_fields = source_fields
#self.setup = settings # dict
# define src/dst cals
sf, ed = cal_trans(sc_time, dst_cal_type, year, month)
# W
DstCal = utime('seconds since %d-1-1' %year, dst_cal_type)
dst_start = DstCal.date2num(datetime(year, month, 1))
dst_end = DstCal.date2num(datetime(year, month, ed, 23, 59, 59))
self.S_cal = utime(sc_time[0]['units'], sc_time[0]['calendar'])
self.D_cal = utime('seconds since %d-1-1' %settings['year_000'],
settings['dst_calendar'])
for date in sc_time:
date['date_num'] = DstCal.date2num(date['date']) * sf
# Get first and last date within range
first_date, last_date = None, None
rev_seq = range(len_sc_time)
rev_seq.reverse()
# Multiple values.. might be broken..
for date in rev_seq:
if sc_time[date]['date_num'] < dst_start:
first_date = date #number..
break
for date in range(len_sc_time):
if sc_time[date]['date_num'] > dst_end:
last_date = date
break
for date in range(first_date, last_date + 1):
nc = Dataset(sc_time[date], 'r')
if key_vec:
pass
#nc_2 = Dataset
# FIX ME
# We shouldnt have to worry about counters
sc_bdy = np.zeros(nvar, sc_z_len, source_ind['ind'].shape[0],
source_ind['ind'].shape[1])
ind_vec = {}
# distinctive variable name since it gets lost in the huge loop
for shoggoth in range(nvar):
varid = nc.variables[var_nam[shoggoth]]
i, ii = source_ind['imin'], source_ind['imax']
j, jj = source_ind['jmin'], source_ind['jmax']
sc_arrays = []
col_sc_arrays = []
if key_vec:
varid_2 = nc_2.variables[var_nam[shoggoth + 1]]
if not isslab and not key_vec:
# NOTE: 0 v 1 indexing may problemate
sc_arrays.append(varid[i-1:ii, j-1:jj, :sc_z_len, :1])
elif key_vec:
sc_arrays.append(varid[i-2:ii, j-1:jj, :sc_z_len, :1])
sc_arrays.append(varid_2[i-1:ii, j-2:jj, :sc_z_len, :1])
for x in 0,1:
# tidy up src array - replace missing val
for y in 'mv', 'fv':
if not np.isnan(sc_fields[y][x]):
ind_vec[y] = sc_arrays[x] == sc_fields[y][x]
sc_arrays[x][ind_vec[y]] = 0
else:
sc_arrays[x][np.isnan(scarr)] = 0
# Adjust for scaling or offsets
if not np.isnan(sc_fields['sf'][x]):
sc_arrays[x] *= sc_fields['sf'][x]
if not np.isnan(sc_fields['os'][x]):
sc_arrays[x] += sc_fields['os'][x]
# Colocate velocity points on T grid prior to rotation
axis = [1, None]
col = 0.5 * (sc_arrays[x][:-axis[0],:-axis[1],:] +
sc_arrays[x][axis[0]:,axis[1]:,:])
col[col == 0] = np.NaN
col_sc_arrays.append(col)
axis.reverse()
# This is a slab
else:
sc_arrays.append(varid[i-1:ii, j-1:jj, :1])
#query var names
if msk and first and shoggoth==0:
pass
# Open another magic file and do stuff
nc3 = Dataset(source_mask, 'r')
varid_3 = nc3.variables['tmaskutil']
msk_array = varid_3[i-1:ii, j-1:jj, :1]
if msk: #must be true for msk array ??...
sc_arrays[0][msk_array == 0] = np.NaN
# Finished reading Source data
#for depth_val in range(sc_z_len):
# tmp_arrays = []
# if not key_vec:
# tmp_arrays.append(sc_arrays[0][:,:depth_val]
def _fv_mv_to_zero(self, scarr, indvec, sc_fields, pos):
for x in 'mv', 'fv':
if not np.isnan(sc_fields[x][pos]):
ind_vec[x] = scarr == sc_fields[x][pos]
scarr[ind_vec[x]] = 0
else:
scarr[np.isnan(scarr)] = 0
return scarr, indvec
# Convert numeric date from source to dest
def convert_date(self, date):
val = self.S_cal.num2date(date)
return self.D_cal.date2num(val)
def cal_trans(self, source, dest, year, month):
vals = {'gregorian': [monthrange(year, month)[1], 31], 'noleap':
[365., 31],'360_day': [360., 30]}
if source not in vals.keys():
raise ValueError('Unknown calendar type: %s' %source)
sf = val[source][0] / val[dest][0]
return sf, vals[dest][1]
pynemo/nemo_coord_gen_pop.py
View file @ 6f50bc0c
......@@ -28,7 +28,7 @@ class Coord:
self.logger = logging.getLogger(__name__)
self.logger.debug( fname )
if not fname:
print 'need some error handling in here or is this redundant?' # TODO
print('need some error handling in here or is this redundant?') # TODO
# Enter define mode
self.ncid = Dataset(fname, 'w', clobber=True, format='NETCDF4')
......
pynemo/profile.py
View file @ 6f50bc0c
......@@ -34,7 +34,7 @@ $Last commit on:$
import time
import logging
import numpy as np
from PyQt4.QtGui import QMessageBox
from PyQt5.QtWidgets import QMessageBox
#Local imports
from pynemo import pynemo_settings_editor
......@@ -244,13 +244,13 @@ def process_bdy(setup_filepath=0, mask_gui=False):
'values in input bdy file')
return
yrs = range(yr_000, yr_end+1)
yrs = list(range(yr_000, yr_end+1))
if yr_end - yr_000 >= 1:
if range(mn_000, mn_end+1) < 12:
if list(range(mn_000, mn_end+1)) < 12:
logger.info('Warning: All months will be extracted as the number '+
'of years is greater than 1')
mns = range(1,13)
mns = list(range(1,13))
else:
mn_000 = settings['month_000']
mn_end = settings['month_end']
......@@ -258,7 +258,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
logging.error('Please check the nn_month_000 and nn_month_end '+
'values in input bdy file')
return
mns = range(mn_000, mn_end+1)
mns = list(range(mn_000, mn_end+1))
# Enter the loop for each year and month extraction
......@@ -311,7 +311,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
# Initialise the mapping indices for each grid
for key, val in emap.items():
for key, val in list(emap.items()):
extract_obj[key] = extract.Extract(Setup.settings,
SourceCoord, DstCoord,
......@@ -324,7 +324,7 @@ def process_bdy(setup_filepath=0, mask_gui=False):
for year in yrs:
for month in mns:
for key, val in emap.items():
for key, val in list(emap.items()):
# Extract the data for a given month and year
......@@ -379,7 +379,7 @@ def write_tidal_data(setup_var, dst_coord_var, grid, tide_cons, cons):
const_name = setup_var.settings['clname'][tide_con]
const_name = const_name.replace("'", "").upper()
for key,val in tmap.items():
for key,val in list(tmap.items()):
fout_tide = setup_var.settings['dst_dir']+ \
setup_var.settings['fn']+ \
......
pynemo/pynemo_exe.py
View file @ 6f50bc0c
......@@ -5,7 +5,7 @@ Entry for the project
'''
import sys, getopt
import profile
from . import profile
import logging
import cProfile
......@@ -21,14 +21,14 @@ def main():
try:
opts, dummy_args = getopt.getopt(sys.argv[1:], "hs:g", ["help","setup=","mask_gui"])
except getopt.GetoptError:
print "usage: pynemo -g -s <namelist.bdy> "
print("usage: pynemo -g -s <namelist.bdy> ")
sys.exit(2)
for opt, arg in opts:
if opt == "-h":
print "usage: pynemo [-g] -s <namelist.bdy> "
print " -g (optional) will open settings editor before extracting the data"
print " -s <bdy filename> file to use"
print("usage: pynemo [-g] -s <namelist.bdy> ")
print(" -g (optional) will open settings editor before extracting the data")
print(" -s <bdy filename> file to use")
sys.exit()
elif opt in ("-s", "--setup"):
setup_file = arg
......@@ -36,7 +36,7 @@ def main():
mask_gui = True
if setup_file == "":
print "usage: pynemo [-g] -s <namelist.bdy> "
print("usage: pynemo [-g] -s <namelist.bdy> ")
sys.exit(2)
#Logger
......@@ -44,7 +44,7 @@ def main():
t0 = time.time()
cProfile.runctx("f(x, y)",{'f': profile.process_bdy, 'x': setup_file, 'y': mask_gui}, {}, 'pynemo_stats')
t1 = time.time()
print "Execution Time: %s" % (t1-t0)
print("Execution Time: %s" % (t1-t0))
if __name__ == "__main__":
main()
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