def on_er_data(self, event):
if self.data_model_num == 2:
if not os.path.isfile(os.path.join(self.WD, 'magic_measurements.txt')):
print('-W- {} is missing'.format(os.path.join(self.WD, 'magic_measurements.txt')))
pw.simple_warning("Your working directory must have a magic_measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file), by combining all imported magnetometer files into one magic_measurements file.")
return False
#self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.ErMagic_data)#,self.Data,self.Data_hierarchy)
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.er_magic)#,self.Data,self.Data_hierarchy)
elif self.data_model_num == 3:
if not os.path.isfile(os.path.join(self.WD, 'measurements.txt')):
pw.simple_warning("Your working directory must have a 3.0. format measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file) and ALSO converted to 3.0., if necessary), then try again.")
return False
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder3(self.WD, self, self.contribution)
self.ErMagic_frame.Show()
self.ErMagic_frame.Center()
size = wx.DisplaySize()
size = (size[0] - 0.3 * size[0], size[1] - 0.3 * size[1]) # gets total available screen space - 10%
self.ErMagic_frame.Raise()
del wait
def on_er_data(self, event):
if self.data_model_num == 2:
if not os.path.isfile(os.path.join(self.WD, 'magic_measurements.txt')):
print('-W- {} is missing'.format(os.path.join(self.WD, 'magic_measurements.txt')))
pw.simple_warning("Your working directory must have a magic_measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file), by combining all imported magnetometer files into one magic_measurements file.")
return False
#self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.ErMagic_data)#,self.Data,self.Data_hierarchy)
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.er_magic)#,self.Data,self.Data_hierarchy)
elif self.data_model_num == 3:
if not os.path.isfile(os.path.join(self.WD, 'measurements.txt')):
pw.simple_warning("Your working directory must have a 3.0. format measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file) and ALSO converted to 3.0., if necessary), then try again.")
return False
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder3(self.WD, self, self.contribution)
self.ErMagic_frame.Show()
self.ErMagic_frame.Center()
size = wx.DisplaySize()
size = (size[0] - 0.3 * size[0], size[1] - 0.3 * size[1]) # gets total available screen space - 10%
self.ErMagic_frame.Raise()
del wait
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print '-I- You already have a grid frame open'
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.Yield()
# hide mainframe
self.on_open_grid_frame()
# make grid frame
self.grid_frame = grid_frame.GridFrame(self.contribution, self.WD, grid_type, grid_type, self.panel)
row_string = ""
# paint validations if appropriate
if self.validation_mode:
if grid_type in self.validation_mode:
self.grid_frame.toggle_help(None, "open")
row_problems = self.failing_items[grid_type]["rows"]
missing_columns = self.failing_items[grid_type]["missing_columns"]
missing_groups = self.failing_items[grid_type]["missing_groups"]
#all_cols = row_problems.columns
#col_nums = range(len(all_cols))
#col_pos = dict(zip(all_cols, col_nums))
if len(row_problems):
row_string = """Columns and rows with problem data have been highlighted in blue.
Cells with problem data are highlighted according to the type of problem.
Red: incorrect data
For full error messages, see {}.""".format(grid_type + "_errors.txt")
for row in row_problems['num']:
self.grid_frame.grid.paint_invalid_row(row)
mask = row_problems["num"] == row
items = row_problems[mask]
cols = items.dropna(how="all", axis=1).drop(["num", "issues"], axis=1)
for col in cols:
pre, col_name = val_up3.extract_col_name(col)
col_ind = self.grid_frame.grid.col_labels.index(col_name)
self.grid_frame.grid.paint_invalid_cell(row, col_ind)
current_label = self.grid_frame.msg_text.GetLabel()
if len(missing_columns):
col_string = "You are missing the following required columns: {}\n\n".format(", ".join(missing_columns))
else:
col_string = ""
if len(missing_groups):
group_string = "You must have at least one column from each of the following groups: {}\n\n".format(", ".join(missing_groups))
else:
group_string = ""
#
add_text = """{}{}{}""".format(col_string, group_string, row_string)
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
self.grid_frame.do_fit(None)
del wait
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print '-I- You already have a grid frame open'
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.Yield()
# hide mainframe
self.on_open_grid_frame()
# make grid frame
self.grid_frame = grid_frame.GridFrame(self.contribution, self.WD, grid_type, grid_type, self.panel)
row_string = ""
# paint validations if appropriate
if self.validation_mode:
if grid_type in self.validation_mode:
self.grid_frame.toggle_help(None, "open")
row_problems = self.failing_items[grid_type]["rows"]
missing_columns = self.failing_items[grid_type]["missing_columns"]
missing_groups = self.failing_items[grid_type]["missing_groups"]
#all_cols = row_problems.columns
#col_nums = range(len(all_cols))
#col_pos = dict(zip(all_cols, col_nums))
if len(row_problems):
row_string = """Columns and rows with problem data have been highlighted in blue.
Cells with problem data are highlighted according to the type of problem.
Red: incorrect data
For full error messages, see {}.""".format(grid_type + "_errors.txt")
for row in row_problems['num']:
self.grid_frame.grid.paint_invalid_row(row)
mask = row_problems["num"] == row
items = row_problems[mask]
cols = items.dropna(how="all", axis=1).drop(["num", "issues"], axis=1)
for col in cols:
pre, col_name = val_up3.extract_col_name(col)
col_ind = self.grid_frame.grid.col_labels.index(col_name)
self.grid_frame.grid.paint_invalid_cell(row, col_ind)
current_label = self.grid_frame.msg_text.GetLabel()
if len(missing_columns):
col_string = "You are missing the following required columns: {}\n\n".format(", ".join(missing_columns))
else:
col_string = ""
if len(missing_groups):
group_string = "You must have at least one column from each of the following groups: {}\n\n".format(", ".join(missing_groups))
else:
group_string = ""
#
add_text = """{}{}{}""".format(col_string, group_string, row_string)
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
self.grid_frame.do_fit(None)
del wait
def __init__(self, WD=None, dmodel=None):
"""
Input working directory, and data model object (optional).
"""
wx.Frame.__init__(self, None, wx.ID_ANY, self.title, name='pmag_gui mainframe')
#set icon
self.icon = wx.Icon()
icon_path = os.path.join(PMAGPY_DIRECTORY, 'programs', 'images', 'PmagPy.ico')
if os.path.isfile(icon_path):
self.icon.CopyFromBitmap(wx.Bitmap(icon_path, wx.BITMAP_TYPE_ANY))
self.SetIcon(self.icon)
else:
print("-I- PmagPy icon file not found -- skipping")
self.data_model = dmodel
self.FIRST_RUN = True
self.panel = wx.Panel(self, name='pmag_gui main panel')
self.InitUI()
# if not specified on the command line,
# make the user choose their working directory
if WD:
self.WD = WD
else:
self.get_dir()
self.get_wd_data()
# use realpath
self.WD = os.path.realpath(self.WD)
# set data model and read in data
self.dir_path.SetValue(self.WD)
# for use as module:
self.resource_dir = os.getcwd()
# set some things
self.HtmlIsOpen = False
self.Bind(wx.EVT_CLOSE, self.on_menu_exit)
# if specified directory doesn't exist, try to make it
try:
if not os.path.exists(self.WD):
os.mkdir(self.WD)
pw.simple_warning("New directory: {}\nwill be created".format(self.WD))
except FileNotFoundError:
pw.simple_warning("You have provided a directory that does not exist and cannot be created.\n Please pick a different directory.")
print("-W- You have provided a directory that does not exist and cannot be created.\n Please pick a different directory.")
# do menubar
menubar = pmag_gui_menu.MagICMenu(self)
self.SetMenuBar(menubar)
self.menubar = menubar
def check_for_meas_file(self):
"""
Check the working directory for a measurement file.
If not found, show a warning and return False.
Otherwise return True.
"""
meas_file_name = "measurements.txt"
dm = "3.0"
if not os.path.isfile(os.path.join(self.WD, meas_file_name)):
pw.simple_warning("Your working directory must have a {} format {} file to run this step. Make sure you have fully completed step 1 (import magnetometer file) and ALSO converted to 3.0., if necessary), then try again.\n\nIf you are trying to look at data downloaded from MagIC, you must unpack the txt file first. Some contributions do not contain measurement data, in which case you won't be able to use this function.".format(dm, meas_file_name))
return False
return True
def on_add_cols(self, event):
"""
Show simple dialog that allows user to add a new column name
"""
col_labels = self.grid.col_labels
dia = pw.ChooseOne(self, yes="Add single columns", no="Add groups")
result1 = dia.ShowModal()
if result1 == wx.ID_CANCEL:
return
elif result1 == wx.ID_YES:
items = [col_name for col_name in self.dm.index if col_name not in col_labels]
dia = pw.HeaderDialog(self, 'columns to add',
items1=list(items), groups=[])
dia.Centre()
result2 = dia.ShowModal()
else:
groups = self.dm['group'].unique()
dia = pw.HeaderDialog(self, 'groups to add',
items1=list(groups), groups=True)
dia.Centre()
result2 = dia.ShowModal()
new_headers = []
if result2 == 5100:
new_headers = dia.text_list
# if there is nothing to add, quit
if not new_headers:
return
if result1 == wx.ID_YES:
# add individual headers
errors = self.add_new_grid_headers(new_headers)
else:
# add header groups
errors = self.add_new_header_groups(new_headers)
if errors:
errors_str = ', '.join(errors)
pw.simple_warning('You are already using the following headers: {}\nSo they will not be added'.format(errors_str))
# problem: if widgets above the grid are too wide,
# the grid does not re-size when adding columns
# awkward solution (causes flashing):
if self.grid.GetWindowStyle() != wx.DOUBLE_BORDER:
self.grid.SetWindowStyle(wx.DOUBLE_BORDER)
self.main_sizer.Fit(self)
self.grid.SetWindowStyle(wx.NO_BORDER)
self.Centre()
self.main_sizer.Fit(self)
#
self.grid.changes = set(range(self.grid.GetNumberRows()))
dia.Destroy()
def on_add_cols(self, event):
"""
Show simple dialog that allows user to add a new column name
"""
col_labels = self.grid.col_labels
dia = pw.ChooseOne(self, yes="Add single columns", no="Add groups")
result1 = dia.ShowModal()
if result1 == wx.ID_CANCEL:
return
elif result1 == wx.ID_YES:
items = [col_name for col_name in self.dm.index if col_name not in col_labels]
dia = pw.HeaderDialog(self, 'columns to add',
items1=list(items), groups=[])
dia.Centre()
result2 = dia.ShowModal()
else:
groups = self.dm['group'].unique()
dia = pw.HeaderDialog(self, 'groups to add',
items1=list(groups), groups=True)
dia.Centre()
result2 = dia.ShowModal()
new_headers = []
if result2 == 5100:
new_headers = dia.text_list
# if there is nothing to add, quit
if not new_headers:
return
if result1 == wx.ID_YES:
# add individual headers
errors = self.add_new_grid_headers(new_headers)
else:
# add header groups
errors = self.add_new_header_groups(new_headers)
if errors:
errors_str = ', '.join(errors)
pw.simple_warning('You are already using the following headers: {}\nSo they will not be added'.format(errors_str))
# problem: if widgets above the grid are too wide,
# the grid does not re-size when adding columns
# awkward solution (causes flashing):
if self.grid.GetWindowStyle() != wx.DOUBLE_BORDER:
self.grid.SetWindowStyle(wx.DOUBLE_BORDER)
self.main_sizer.Fit(self)
self.grid.SetWindowStyle(wx.NO_BORDER)
self.Centre()
self.main_sizer.Fit(self)
#
self.grid.changes = set(range(self.grid.GetNumberRows()))
dia.Destroy()
def check_for_meas_file(self):
"""
Check the working directory for a measurement file.
If not found, show a warning and return False.
Otherwise return True.
"""
if self.data_model_num == 2:
meas_file_name = "magic_measurements.txt"
dm = "2.5"
else:
meas_file_name = "measurements.txt"
dm = "3.0"
if not os.path.isfile(os.path.join(self.WD, meas_file_name)):
pw.simple_warning("Your working directory must have a {} format {} file to run this step. Make sure you have fully completed step 1 (import magnetometer file) and ALSO converted to 3.0., if necessary), then try again.\n\nIf you are trying to look at data downloaded from MagIC, you must unpack the txt file first. Some contributions do not contain measurement data, in which case you won't be able to use this function.".format(dm, meas_file_name))
return False
return True
def on_er_data(self, event):
if not os.path.isfile(os.path.join(self.WD, 'magic_measurements.txt')):
import dialogs.pmag_widgets as pw
pw.simple_warning("Your working directory must have a magic_measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file), by combining all imported magnetometer files into one magic_measurements file.")
return False
#self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.ErMagic_data)#,self.Data,self.Data_hierarchy)
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.er_magic)#,self.Data,self.Data_hierarchy)
self.ErMagic_frame.Show()
self.ErMagic_frame.Center()
size = wx.DisplaySize()
size = (size[0] - 0.3 * size[0], size[1] - 0.3 * size[1]) # gets total available screen space - 10%
self.ErMagic_frame.Raise()
del wait
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print '-I- You already have a grid frame open'
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(
event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.Yield()
# hide mainframe
self.on_open_grid_frame()
self.grid_frame = grid_frame.GridFrame(self.er_magic, self.WD,
grid_type, grid_type,
self.panel)
if self.validation_mode:
if grid_type in self.validation_mode:
self.grid_frame.grid.paint_invalid_cells(
self.warn_dict[grid_type])
#self.grid_frame.msg_boxsizer
current_label = self.grid_frame.msg_text.GetLabel()
add_text = """\n\nColumns and rows with problem data have been highlighted in blue.
Cells with problem data are highlighted with different colors according to the type of problem.
Red: missing required data
Green: missing or invalid parent
Blue: non-numeric data provided in a numeric field
Gray: unrecognized column
Purple: invalid result child
Yellow: Out-of-range latitude (should be -90 - 90) or longitude (should be 0-360)
Light gray: Unrecognized term in controlled vocabulary
Note: It is possible to have a row highlighted that has no highlighted column.
This means that you are missing information higher up in the data.
For example: a specimen could be missing a site name.
However, you need to fix this in the sample grid, not the specimen grid.
Once each item in the data has its proper parent, validations will be correct.
"""
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
del wait
def check_for_meas_file(self):
"""
Check the working directory for a measurement file.
If not found, show a warning and return False.
Otherwise return True.
"""
if self.data_model_num == 2:
meas_file_name = "magic_measurements.txt"
dm = "2.5"
else:
meas_file_name = "measurements.txt"
dm = "3.0"
if not os.path.isfile(os.path.join(self.WD, meas_file_name)):
pw.simple_warning(
"Your working directory must have a {} format {} file to run this step. Make sure you have fully completed step 1 (import magnetometer file) and ALSO converted to 3.0., if necessary), then try again."
.format(dm, meas_file_name))
return False
return True
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print('-I- You already have a grid frame open')
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.SafeYield()
# hide mainframe
self.on_open_grid_frame()
self.grid_frame = grid_frame.GridFrame(self.er_magic, self.WD, grid_type, grid_type, self.panel)
if self.validation_mode:
if grid_type in self.validation_mode:
self.grid_frame.grid.paint_invalid_cells(self.warn_dict[grid_type])
#self.grid_frame.msg_boxsizer
current_label = self.grid_frame.msg_text.GetLabel()
add_text = """\n\nColumns and rows with problem data have been highlighted in blue.
Cells with problem data are highlighted with different colors according to the type of problem.
Red: missing required data
Green: missing or invalid parent
Blue: non-numeric data provided in a numeric field
Gray: unrecognized column
Purple: invalid result child
Yellow: Out-of-range latitude (should be -90 - 90) or longitude (should be 0-360)
Light gray: Unrecognized term in controlled vocabulary
Note: It is possible to have a row highlighted that has no highlighted column.
This means that you are missing information higher up in the data.
For example: a specimen could be missing a site name.
However, you need to fix this in the sample grid, not the specimen grid.
Once each item in the data has its proper parent, validations will be correct.
"""
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
del wait
def get_dm_num(self):
"""
Show dialog to get user input for which data model to use,
2 or 3.
Set self.data_model_num, and create 3.0 contribution or
2.5 ErMagicBuilder as needed.
"""
ui_dialog = demag_dialogs.user_input(self,['data_model'],
parse_funcs=[float],
heading="Please input prefered data model (2.5,3.0). Note: 2.5 is for legacy projects only, if you have new data OR if you want to upgrade your old data, please use 3.0.",
values=[3])
# figure out where to put this
res = ui_dialog.ShowModal()
vals = ui_dialog.get_values()
self.data_model_num = int(vals[1]['data_model'])
#
if self.data_model_num not in (2, 3):
pw.simple_warning("Input data model not recognized, defaulting to 3")
self.data_model_num = 3
self.set_dm(self.data_model_num)
def get_dm_num(self):
"""
Show dialog to get user input for which data model to use,
2 or 3.
Set self.data_model_num, and create 3.0 contribution or
2.5 ErMagicBuilder as needed.
"""
ui_dialog = demag_dialogs.user_input(self,['data_model'],
parse_funcs=[float],
heading="Please input prefered data model (2.5,3.0). Note: 2.5 is for legacy projects only, if you have new data OR if you want to upgrade your old data, please use 3.0.",
values=[3])
# figure out where to put this
res = ui_dialog.ShowModal()
vals = ui_dialog.get_values()
self.data_model_num = int(vals[1]['data_model'])
#
if self.data_model_num not in (2, 3):
pw.simple_warning("Input data model not recognized, defaulting to 3")
self.data_model_num = 3
self.set_dm(self.data_model_num)
def remove_col_label(self, event):
"""
check to see if column is required
if it is not, delete it from grid
"""
col = event.GetCol()
label = self.grid.GetColLabelValue(col)
if '**' in label:
label = label.strip('**')
elif '^^' in label:
label = label.strip('^^')
if label in self.reqd_headers:
pw.simple_warning("That header is required, and cannot be removed")
return False
else:
print('That header is not required:', label)
self.grid.remove_col(col)
del self.contribution.tables[self.grid_type].df[label]
# causes resize on each column header delete
# can leave this out if we want.....
self.main_sizer.Fit(self)
def on_er_data(self, event):
if not os.path.isfile(os.path.join(self.WD, 'magic_measurements.txt')):
import dialogs.pmag_widgets as pw
pw.simple_warning(
"Your working directory must have a magic_measurements.txt file to run this step. Make sure you have fully completed step 1 (import magnetometer file), by combining all imported magnetometer files into one magic_measurements file."
)
return False
#self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(self.WD, self, self.ErMagic_data)#,self.Data,self.Data_hierarchy)
wait = wx.BusyInfo('Compiling required data, please wait...')
wx.Yield()
self.ErMagic_frame = ErMagicBuilder.MagIC_model_builder(
self.WD, self, self.er_magic) #,self.Data,self.Data_hierarchy)
self.ErMagic_frame.Show()
self.ErMagic_frame.Center()
size = wx.DisplaySize()
size = (size[0] - 0.3 * size[0], size[1] - 0.3 * size[1]
) # gets total available screen space - 10%
self.ErMagic_frame.Raise()
del wait
def remove_col_label(self, event):
"""
check to see if column is required
if it is not, delete it from grid
"""
col = event.GetCol()
label = self.grid.GetColLabelValue(col)
if '**' in label:
label = label.strip('**')
elif '^^' in label:
label = label.strip('^^')
if label in self.reqd_headers:
pw.simple_warning("That header is required, and cannot be removed")
return False
else:
print('That header is not required:', label)
self.grid.remove_col(col)
del self.contribution.tables[self.grid_type].df[label]
# causes resize on each column header delete
# can leave this out if we want.....
self.main_sizer.Fit(self)
def __init__(self, WD=None, DM=None, dmodel=None):
"""
Input working directory, data model number (2.5 or 3),
and data model (optional).
"""
wx.Frame.__init__(self, None, wx.ID_ANY, self.title, name='pmag_gui mainframe')
#set icon
self.icon = wx.Icon()
icon_path = os.path.join(PMAGPY_DIRECTORY, 'programs', 'images', 'PmagPy.ico')
if os.path.isfile(icon_path):
self.icon.CopyFromBitmap(wx.Bitmap(icon_path, wx.BITMAP_TYPE_ANY))
self.SetIcon(self.icon)
else:
print("-I- PmagPy icon file not found -- skipping")
# if DM was provided:
if DM:
self.data_model_num = int(float(DM))
else:
self.data_model_num = 3
# check that self.data_model is valid, otherwise default 3
if self.data_model_num not in [2, 3]:
pw.simple_warning("Input data model number {} not recognized, defaulting to 3".format(str(self.data_model_num)))
self.data_model_num = 3
self.data_model = dmodel
self.FIRST_RUN = True
self.panel = wx.Panel(self, name='pmag_gui main panel')
self.InitUI()
# if not specified on the command line,
# make the user choose their working directory
if WD:
self.WD = WD
else:
self.get_dir()
# use realpath
self.WD = os.path.realpath(self.WD)
# set data model and read in data
self.set_dm(self.data_model_num)
self.dir_path.SetValue(self.WD)
# for use as module:
self.resource_dir = os.getcwd()
# set some things
self.HtmlIsOpen = False
self.Bind(wx.EVT_CLOSE, self.on_menu_exit)
# if specified directory doesn't exist, try to make it
try:
if not os.path.exists(self.WD):
os.mkdir(self.WD)
pw.simple_warning("New directory: {}\nwill be created".format(self.WD))
except FileNotFoundError:
pw.simple_warning("You have provided a directory that does not exist and cannot be created.\n Please pick a different directory.")
print("-W- You have provided a directory that does not exist and cannot be created.\n Please pick a different directory.")
def on_btn_upload(self, event):
"""
Try to run upload_magic.
Open validation mode if the upload file has problems.
"""
if not self.check_for_uncombined_files():
return
outstring = "upload_magic.py"
print("-I- running python script:\n %s" % (outstring))
wait = wx.BusyInfo("Please wait, working...")
wx.SafeYield()
success_responses = ['200', 200, '201', 201, True]
if 'measurements' in self.contribution.tables:
self.contribution.tables['measurements'].add_measurement_names()
upload_file, val_response, dummy1, dummy2 = ipmag.upload_magic(
concat=False, input_dir_path=self.WD, dir_path=self.WD)
del wait
if val_response == "no 3.0 files found, upload file not created":
pw.simple_warning(
"No 3.0 files were found in your directory, so no upload could be created!"
)
return
status = val_response['status']
if not status:
pw.simple_warning(
"Oops, something went wrong with validating on the server.\n{}\nTry again later or submit a bug report."
.format(val_response['warnings']))
return
validation_errors = val_response['validation']
if (not validation_errors['warnings']) and (
not validation_errors['errors']):
text = "You are ready to upload!\n{} was generated in {}".format(
os.path.split(upload_file)[1], self.WD)
dlg = pw.ChooseOne(self, "Go to MagIC for uploading",
"Not ready yet", text, "Saved")
dlg.Centre()
result = dlg.ShowModal()
if result == wx.ID_OK:
dlg.Destroy()
if result == wx.ID_YES:
pw.on_database_upload(None)
return
# there were problems, so display validation
text = "There were some problems with the creation of your upload file.\nSee Terminal/message window for details"
dlg = wx.MessageDialog(self,
caption="Error",
message=text,
style=wx.OK)
dlg.Centre()
result = dlg.ShowModal()
# TODO: get the error-y business formatted into a dict of lists of dicts
from programs import magic_gui
self.Disable()
self.Hide()
self.magic_gui_frame = magic_gui.MainFrame(
self.WD,
dmodel=self.data_model,
title="Validations",
contribution=self.contribution,
errors=validation_errors['errors'])
self.magic_gui_frame.Centre()
self.magic_gui_frame.Show()
self.magic_gui_frame.highlight_problems()
# bind that button to quitting magic gui and re-enabling Pmag GUI
self.magic_gui_frame.Bind(wx.EVT_BUTTON, self.on_end_validation,
self.magic_gui_frame.return_btn)
# do binding so that closing/quitting re-opens the main frame
self.magic_gui_frame.Bind(wx.EVT_CLOSE, self.on_end_validation)
# this makes it work with only the validation window open
self.magic_gui_frame.Bind(
wx.EVT_MENU,
lambda event: self.menubar.on_quit(event, self.magic_gui_frame),
self.magic_gui_frame.menubar.file_quit)
# this makes it work if an additional grid is open
self.Bind(
wx.EVT_MENU,
lambda event: self.menubar.on_quit(event, self.magic_gui_frame),
self.magic_gui_frame.menubar.file_quit)
def on_okButton(self, event):
meas_files = []
spec_files = []
samp_files = []
site_files = []
loc_files = []
for i in range(self.max_files):
# read directory path
dirpath = self.dir_paths[i].GetValue()
if dirpath != "":
dir_name = os.path.realpath(dirpath)
#dir_name = str(dirpath.split("/")[-1])
else:
continue
# get location
location_name = self.file_locations[i].GetValue()
# get sample-specimen naming convention
samp_con = str(self.naming_con_boxes[i].GetValue())
samp_chars = str(self.naming_con_char[i].GetValue())
samp_chars = samp_chars.strip('"').strip("'")
if samp_con == "character delimited" and not samp_chars:
pw.simple_warning(
"To delimit samples by character, you must provide the delimiter, (eg. \"-\" or \"_\")!"
)
return
# get site-sample naming convention
site_con = str(self.site_name_conventions[i].GetValue())
site_chars = str(self.site_name_chars[i].GetValue())
site_chars = site_chars.strip('"').strip("'")
if site_con == "character delimited" and not site_chars:
pw.simple_warning(
"To delimit sites by character, you must provide the delimiter, (eg. \"-\" or \"_\")!"
)
return
# name output files
if self.data_model_num == 2:
meas_out = "magic_measurements_{}.txt".format(i)
spec_out = "er_specimens_{}.txt".format(i)
samp_out = "er_samples_{}.txt".format(i)
site_out = "er_sites_{}.txt".format(i)
loc_out = "er_locations_{}.txt".format(i)
else:
meas_out = "measurements_{}.txt".format(i)
spec_out = "specimens_{}.txt".format(i)
samp_out = "samples_{}.txt".format(i)
site_out = "sites_{}.txt".format(i)
loc_out = "locations_{}.txt".format(i)
# do conversion
convert.livdb(dir_name, self.WD, meas_out, spec_out, samp_out,
site_out, loc_out, samp_con, samp_chars, site_con,
site_chars, location_name)
meas_files.append(meas_out)
spec_files.append(spec_out)
samp_files.append(samp_out)
site_files.append(site_out)
loc_files.append(loc_out)
if self.data_model_num == 2:
res = ipmag.combine_magic(meas_files, "magic_measurements.txt", 2)
ipmag.combine_magic(spec_files, "er_specimens.txt", 2)
else:
res = ipmag.combine_magic(meas_files, "measurements.txt", 3)
ipmag.combine_magic(spec_files, "specimens.txt", 3)
ipmag.combine_magic(samp_files, "samples.txt", 3)
ipmag.combine_magic(site_files, "sites.txt", 3)
ipmag.combine_magic(loc_files, "locations.txt", 3)
pmag.remove_files(meas_files)
pmag.remove_files(spec_files)
pmag.remove_files(samp_files)
pmag.remove_files(site_files)
pmag.remove_files(loc_files)
if res:
self.after_convert_dia()
else:
pw.simple_warning(
"Something when wrong with one or more of your files.\nSee Terminal/Command Prompt output for more details"
)
def onImport(self, event):
"""
Import a MagIC-format file
"""
if self.grid.changes:
print("-W- Your changes will be overwritten...")
wind = pw.ChooseOne(self, "Import file anyway", "Save grid first",
"-W- Your grid has unsaved changes which will be overwritten if you import a file now...")
wind.Centre()
res = wind.ShowModal()
# save grid first:
if res == wx.ID_NO:
self.onSave(None, alert=True, destroy=False)
# reset self.changes
self.grid.changes = set()
openFileDialog = wx.FileDialog(self, "Open MagIC-format file", self.WD, "",
"MagIC file|*.*", wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
result = openFileDialog.ShowModal()
if result == wx.ID_OK:
# get filename
filename = openFileDialog.GetPath()
# make sure the dtype is correct
f = open(filename)
line = f.readline()
if line.startswith("tab"):
delim, dtype = line.split("\t")
else:
delim, dtype = line.split("")
f.close()
dtype = dtype.strip()
if (dtype != self.grid_type) and (dtype + "s" != self.grid_type):
text = "You are currently editing the {} grid, but you are trying to import a {} file.\nPlease open the {} grid and then re-try this import.".format(self.grid_type, dtype, dtype)
pw.simple_warning(text)
return
# grab old data for concatenation
if self.grid_type in self.contribution.tables:
old_df_container = self.contribution.tables[self.grid_type]
else:
old_df_container = None
old_col_names = self.grid.col_labels
# read in new file and update contribution
df_container = nb.MagicDataFrame(filename, dmodel=self.dm,
columns=old_col_names)
# concatenate if possible
if not isinstance(old_df_container, type(None)):
df_container.df = pd.concat([old_df_container.df, df_container.df],
axis=0)
self.contribution.tables[df_container.dtype] = df_container
self.grid_builder = GridBuilder(self.contribution, self.grid_type,
self.panel, parent_type=self.parent_type,
reqd_headers=self.reqd_headers)
# delete old grid
self.grid_box.Hide(0)
self.grid_box.Remove(0)
# create new, updated grid
self.grid = self.grid_builder.make_grid()
self.grid.InitUI()
# add data to new grid
self.grid_builder.add_data_to_grid(self.grid, self.grid_type)
# add new grid to sizer and fit everything
self.grid_box.Add(self.grid, flag=wx.ALL, border=5)
self.main_sizer.Fit(self)
self.Centre()
# add any needed drop-down-menus
self.drop_down_menu = drop_down_menus.Menus(self.grid_type,
self.contribution,
self.grid)
# done!
return
def __init__(self, WD=None, DM=None, dmodel=None):
"""
Input working directory, data model number (2.5 or 3),
and data model (optional).
"""
wx.Frame.__init__(self,
None,
wx.ID_ANY,
self.title,
name='pmag_gui mainframe')
#set icon
self.icon = wx.Icon()
icon_path = os.path.join(PMAGPY_DIRECTORY, 'programs', 'images',
'PmagPy.ico')
if os.path.isfile(icon_path):
self.icon.CopyFromBitmap(wx.Bitmap(icon_path, wx.BITMAP_TYPE_ANY))
self.SetIcon(self.icon)
else:
print("-I- PmagPy icon file not found -- skipping")
# if DM was provided:
if DM:
self.data_model_num = int(float(DM))
# try to get DM from command line args
if not DM:
self.data_model_num = int(float(pmag.get_named_arg("-DM", 0)))
DM = self.data_model_num
# if WD was provided:
if WD:
self.WD = WD
else:
WD = pmag.get_named_arg("-WD", '')
self.WD = WD
self.WD = os.path.realpath(self.WD)
self.data_model = dmodel
self.FIRST_RUN = True
self.panel = wx.Panel(self, name='pmag_gui main panel')
self.InitUI()
if WD and DM:
self.set_dm(self.data_model_num)
if WD:
self.dir_path.SetValue(self.WD)
# for use as module:
self.resource_dir = os.getcwd()
# set some things
self.HtmlIsOpen = False
self.Bind(wx.EVT_CLOSE, self.on_menu_exit)
# if not specified on the command line,
# make the user choose data model num (2 or 3)
# and working directory
wx.CallAfter(self.get_dm_and_wd, DM, WD)
# if specified directory doesn't exist, try to make it
try:
if not os.path.exists(self.WD):
os.mkdir(self.WD)
pw.simple_warning("New directory: {}\nwill be created".format(
self.WD))
except FileNotFoundError:
pw.simple_warning(
"You have provided a directory that does not exist and cannot be created.\n Please pick a different directory."
)
print(
"-W- You have provided a directory that does not exist and cannot be created.\n Please pick a different directory."
)
def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line optins]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe([ ['f', False, 'magic_measurements.txt'], ['fsum', False, ''],
['fwig', False, ''], ['fsa', False, ''],
['fa', False, ''], ['fsp', False, ''],
['fres', False, '' ], ['fmt', False, 'svg'],
['LP', False, ''], ['n', False, False],
['d', False, '-1 -1'], ['ts', False, ''],
['WD', False, '.'], ['L', False, True],
['S', False, True], ['D', False, True],
['I', False, True], ['M', False, True],
['log', False, 0],
['ds', False, 'sample_core_depth'],
['sym', False, 'bo 5'], ['ID', False, '.'],
['sav', False, False]])
checked_args = extractor.extract_and_check_args(args, dataframe)
meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol, input_dir, save = extractor.get_vars(['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym', 'ID', 'sav'], checked_args)
# format some variables
# format symbol/size
try:
sym, size = symbol.split()
size = int(size)
except:
print('you should provide -sym in this format: ro 5')
print('using defaults instead')
sym, size = 'ro', 5
# format result file, symbol, size
if res_file:
try:
res_file, res_sym, res_size = res_file.split()
except:
print('you must provide -fres in this format: -fres filename symbol size')
print('could not parse {}, defaulting to using no result file'.format(res_file))
res_file, res_sym, res_size = '', '', 0
else:
res_file, res_sym, res_size = '', '', 0
# format specimen file, symbol, size
if spc_file:
try:
spc_file, spc_sym, spc_size = spc_file.split()
except:
print('you must provide -fsp in this format: -fsp filename symbol size')
print('could not parse {}, defaulting to using no specimen file'.format(spc_file))
spc_file, spc_sym, spc_size = '', '', 0
else:
spc_file, spc_sym, spc_size = '', '', 0
# format min/max depth
try:
dmin, dmax = depth.split()
except:
print('you must provide -d in this format: -d dmin dmax')
print('could not parse {}, defaulting to plotting all depths'.format(depth))
dmin, dmax = -1, -1
# format timescale, min/max time
if timescale:
try:
timescale, amin, amax = timescale.split()
pltTime = True
except:
print('you must provide -ts in this format: -ts timescale minimum_age maximum_age')
print('could not parse {}, defaulting to using no timescale'.format(timescale))
timescale, amin, amax = None, -1, -1
pltTime = False
else:
timescale, amin, amax = None, -1, -1
pltTime = False
# format norm and wt_file
if norm and not isinstance(norm, bool):
wt_file = norm
norm = True
else:
norm = False
wt_file = ''
# format list of protcols and step
try:
method, step = meth.split()
except:
print('To use the -LP flag you must provide both the protocol and the step in this format:\n-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot')
print('Defaulting to using no protocol')
method, step = 'LT-NO', 0
# list of varnames
#['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym' ]
#meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol
fig, figname = ipmag.core_depthplot(input_dir, meas_file, spc_file, samp_file, age_file, sum_file, wt_file, depth_scale, dmin, dmax, sym, size, spc_sym, spc_size, method, step, fmt, pltDec, pltInc, pltMag, pltLine, pltSus, logit, pltTime, timescale, amin, amax, norm)
if not pmagplotlib.isServer:
figname = figname.replace(':', '_')
if fig and save:
plt.savefig(figname)
return
app = wx.App(redirect=False)
if not fig:
pw.simple_warning('No plot was able to be created with the data you provided.\nMake sure you have given all the required information and try again')
return False
dpi = fig.get_dpi()
pixel_width = dpi * fig.get_figwidth()
pixel_height = dpi * fig.get_figheight()
figname = os.path.join(dir_path, figname)
plot_frame = pmag_menu_dialogs.PlotFrame((int(pixel_width), int(pixel_height + 50)),
fig, figname, standalone=True)
app.MainLoop()
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, V1_dec, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
# or, for Anaconda users:
ani_depthplot_anaconda [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic (MagIC 2 only)
-fb FILE: specify input measurements format file from magic
-fsa FILE: specify input sample format file from magic
-fsp FILE: specify input specimen file (MagIC 3 only)
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf (core depth)
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: rmag_anisotropy.txt
Bulk susceptibility file: magic_measurements.txt
Samples file: er_samples.txt
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe(
[['f', False, 'rmag_anisotropy.txt'],
['fb', False, 'magic_measurements.txt'],
['fsa', False, 'er_samples.txt'], ['fa', False, None],
['fsum', False, None], ['fmt', False, 'svg'], ['ds', False, 'mbsf'],
['d', False, '-1 -1'], ['sav', False, False], ['WD', False, '.'],
['DM', False, 3], ['fsp', False, 'specimens.txt']])
#args = sys.argv
checked_args = extractor.extract_and_check_args(args, dataframe)
ani_file, meas_file, samp_file, age_file, sum_file, fmt, depth_scale, depth, save_quietly, dir_path, data_model, spec_file = extractor.get_vars(
[
'f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD',
'DM', 'fsp'
], checked_args)
# format min/max depth
try:
dmin, dmax = depth.split()
dmin, dmax = float(dmin), float(dmax)
except:
print('you must provide depth in this format: -d dmin dmax')
print('could not parse "{}", defaulting to plotting all depths'.format(
'-d ' + str(depth)))
dmin, dmax = -1, -1
if depth_scale:
if depth_scale not in ['age', 'mbsf', 'mcd']:
print(
'-W- Unrecognized option "{}" provided for depth scale.\n Options for depth scale are mbsf (meters below sea floor) or mcd (meters composite depth).\n Alternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\n Using default "mbsf"'
.format(depth_scale))
depth_scale = 'sample_core_depth'
if age_file:
depth_scale = 'age'
elif 'mbsf' in depth_scale:
depth_scale = 'sample_core_depth'
elif 'mcd' in depth_scale:
depth_scale = 'sample_composite_depth'
data_model = int(float(data_model))
# MagIC 2
if data_model == 2:
fig, figname = ipmag.ani_depthplot2(ani_file, meas_file, samp_file,
age_file, sum_file, fmt, dmin,
dmax, depth_scale, dir_path)
# MagIC 3
else:
if meas_file == "magic_measurements.txt":
meas_file = 'measurements.txt'
if samp_file in ['er_samples.txt', 'pmag_samples.txt']:
samp_file = "samples.txt"
site_file = 'sites.txt'
fig, figname = ipmag.ani_depthplot(spec_file, samp_file, meas_file,
site_file, age_file, sum_file, fmt,
dmin, dmax, depth_scale, dir_path)
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
plt.savefig(figname)
plt.clf()
print('Saved file: {}'.format(figname))
return False
app = wx.App(redirect=False)
if not fig:
pw.simple_warning(
'No plot was able to be created with the data you provided.\nMake sure you have given all the required information and try again'
)
return False
dpi = fig.get_dpi()
pixel_width = dpi * fig.get_figwidth()
pixel_height = dpi * fig.get_figheight()
figname = os.path.join(dir_path, figname)
plot_frame = pmag_menu_dialogs.PlotFrame(
(int(pixel_width), int(pixel_height + 50)),
fig,
figname,
standalone=True)
app.MainLoop()
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print('-I- You already have a grid frame open')
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.Yield()
# propagate site lat/lon info into locations if necessary
if grid_type == 'locations' and 'sites' in self.contribution.tables:
self.contribution.get_min_max_lat_lon()
self.contribution.propagate_cols_up(['lithologies',
'geologic_classes'],
'locations', 'sites')
# propagate lithologies/type/class information from sites to samples/specimens
if grid_type in ['specimens', 'samples']:
self.contribution.propagate_lithology_cols()
# propagate average lat/lon info from samples table if
# available in samples and missing in sites
if grid_type == 'sites':
self.contribution.propagate_average_up(cols=['lat', 'lon', 'height'],
target_df_name='sites',
source_df_name='samples')
self.contribution.propagate_lithology_cols()
# hide mainframe
self.on_open_grid_frame()
# choose appropriate size for grid
if grid_type == 'measurements':
huge = True
else:
huge = False
# make grid frame
self.grid_frame = grid_frame.GridFrame(self.contribution, self.WD,
grid_type, grid_type,
self.panel, huge=huge)
row_string = ""
# paint validations if appropriate
if self.validation_mode:
if grid_type in self.validation_mode:
if grid_type == 'measurements':
skip_cell_render = True
else:
skip_cell_render = False
self.grid_frame.toggle_help(None, "open")
row_problems = self.failing_items[grid_type]["rows"]
missing_columns = self.failing_items[grid_type]["missing_columns"]
missing_groups = self.failing_items[grid_type]["missing_groups"]
#all_cols = row_problems.columns
#col_nums = range(len(all_cols))
#col_pos = dict(zip(all_cols, col_nums))
if len(row_problems):
row_string = "Columns and rows with problem data have been highlighted in blue.\n"
if not skip_cell_render:
row_string += "Cells with problem data are highlighted according to the type of problem.\nRed: incorrect data\n"
row_string += "For full error messages, see {}.".format(grid_type + "_errors.txt")
for row in row_problems['num']:
self.grid_frame.grid.paint_invalid_row(row)
mask = row_problems["num"] == row
items = row_problems[mask]
cols = items.dropna(how="all", axis=1).drop(["num", "issues"], axis=1)
for col in cols:
pre, col_name = val_up3.extract_col_name(col)
col_ind = self.grid_frame.grid.col_labels.index(col_name)
self.grid_frame.grid.paint_invalid_cell(row, col_ind,
skip_cell=skip_cell_render)
current_label = self.grid_frame.msg_text.GetLabel()
if len(missing_columns):
col_string = "You are missing the following required columns: {}\n\n".format(", ".join(missing_columns))
else:
col_string = ""
if len(missing_groups):
group_string = "You must have at least one column from each of the following groups: {}\n\n".format(", ".join(missing_groups))
else:
group_string = ""
#
add_text = """{}{}{}""".format(col_string, group_string, row_string)
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
self.grid_frame.do_fit(None)
del wait
def onImport(self, event):
"""
Import a MagIC-format file
"""
if self.grid.changes:
print("-W- Your changes will be overwritten...")
wind = pw.ChooseOne(self, "Import file anyway", "Save grid first",
"-W- Your grid has unsaved changes which will be overwritten if you import a file now...")
wind.Centre()
res = wind.ShowModal()
# save grid first:
if res == wx.ID_NO:
self.onSave(None, alert=True, destroy=False)
# reset self.changes
self.grid.changes = set()
openFileDialog = wx.FileDialog(self, "Open MagIC-format file", self.WD, "",
"MagIC file|*.*", wx.FD_OPEN | wx.FD_FILE_MUST_EXIST)
result = openFileDialog.ShowModal()
if result == wx.ID_OK:
# get filename
filename = openFileDialog.GetPath()
# make sure the dtype is correct
f = open(filename)
line = f.readline()
if line.startswith("tab"):
delim, dtype = line.split("\t")
else:
delim, dtype = line.split("")
f.close()
dtype = dtype.strip()
if (dtype != self.grid_type) and (dtype + "s" != self.grid_type):
text = "You are currently editing the {} grid, but you are trying to import a {} file.\nPlease open the {} grid and then re-try this import.".format(self.grid_type, dtype, dtype)
pw.simple_warning(text)
return
# grab old data for concatenation
if self.grid_type in self.contribution.tables:
old_df_container = self.contribution.tables[self.grid_type]
else:
old_df_container = None
old_col_names = self.grid.col_labels
# read in new file and update contribution
df_container = nb.MagicDataFrame(filename, dmodel=self.dm,
columns=old_col_names)
# concatenate if possible
if not isinstance(old_df_container, type(None)):
df_container.df = pd.concat([old_df_container.df, df_container.df],
axis=0)
self.contribution.tables[df_container.dtype] = df_container
self.grid_builder = GridBuilder(self.contribution, self.grid_type,
self.panel, parent_type=self.parent_type,
reqd_headers=self.reqd_headers)
# delete old grid
self.grid_box.Hide(0)
self.grid_box.Remove(0)
# create new, updated grid
self.grid = self.grid_builder.make_grid()
self.grid.InitUI()
# add data to new grid
self.grid_builder.add_data_to_grid(self.grid, self.grid_type)
# add new grid to sizer and fit everything
self.grid_box.Add(self.grid, flag=wx.ALL, border=5)
self.main_sizer.Fit(self)
self.Centre()
# add any needed drop-down-menus
self.drop_down_menu = drop_down_menus.Menus(self.grid_type,
self.contribution,
self.grid)
# done!
return
def main():
"""
NAME
core_depthplot.py
DESCRIPTION
plots various measurements versus core_depth or age. plots data flagged as 'FS-SS-C' as discrete samples.
SYNTAX
core_depthplot.py [command line options]
# or, for Anaconda users:
core_depthplot_anaconda [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input magic_measurments format file from magi
-fsum FILE: specify input LIMS database (IODP) core summary csv file
-fwig FILE: specify input depth,wiggle to plot, in magic format with sample_core_depth key for depth
-fsa FILE: specify input er_samples format file from magic for depth
-fa FILE: specify input er_ages format file from magic for age
NB: must have either -fsa OR -fa (not both)
-fsp FILE sym size: specify input zeq_specimen format file from magic, sym and size
NB: PCAs will have specified color, while fisher means will be white with specified color as the edgecolor
-fres FILE specify input pmag_results file from magic, sym and size
-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot
-S do not plot blanket treatment data (if this is set, you don't need the -LP)
-sym SYM SIZE, symbol, size for continuous points (e.g., ro 5, bs 10, g^ 10 for red dot, blue square, green triangle), default is blue dot at 5 pt
-D do not plot declination
-M do not plot magnetization
-log plot magnetization on a log scale
-L do not connect dots with a line
-I do not plot inclination
-d min max [in m] depth range to plot
-n normalize by weight in er_specimen table
-Iex: plot the expected inc at lat - only available for results with lat info in file
-ts TS amin amax: plot the GPTS for the time interval between amin and amax (numbers in Ma)
TS: [ck95, gts04, gts12]
-ds [mbsf,mcd] specify depth scale, mbsf default
-fmt [svg, eps, pdf, png] specify output format for plot (default: svg)
-sav save plot silently
DEFAULTS:
Measurements file: magic_measurements.txt
Samples file: er_samples.txt
NRM step
Summary file: none
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe([ ['f', False, 'magic_measurements.txt'], ['fsum', False, ''],
['fwig', False, ''], ['fsa', False, ''],
['fa', False, ''], ['fsp', False, ''],
['fres', False, '' ], ['fmt', False, 'svg'],
['LP', False, ''], ['n', False, False],
['d', False, '-1 -1'], ['ts', False, ''],
['WD', False, '.'], ['L', False, True],
['S', False, True], ['D', False, True],
['I', False, True], ['M', False, True],
['log', False, 0],
['ds', False, 'sample_core_depth'],
['sym', False, 'bo 5'], ['ID', False, '.'],
['sav', False, False], ['DM', False, 3]])
checked_args = extractor.extract_and_check_args(args, dataframe)
meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol, input_dir, save, data_model_num = extractor.get_vars(
['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym', 'ID', 'sav', 'DM'], checked_args)
# format some variables
# format symbol/size
try:
sym, size = symbol.split()
size = int(size)
except:
print('you should provide -sym in this format: ro 5')
print('using defaults instead')
sym, size = 'ro', 5
# format result file, symbol, size
if res_file:
try:
res_file, res_sym, res_size = res_file.split()
except:
print('you must provide -fres in this format: -fres filename symbol size')
print(
'could not parse {}, defaulting to using no result file'.format(res_file))
res_file, res_sym, res_size = '', '', 0
else:
res_file, res_sym, res_size = '', '', 0
# format specimen file, symbol, size
if spc_file:
try:
spc_file, spc_sym, spc_size = spc_file.split()
except:
print('you must provide -fsp in this format: -fsp filename symbol size')
print(
'could not parse {}, defaulting to using no specimen file'.format(spc_file))
spc_file, spc_sym, spc_size = '', '', 0
else:
spc_file, spc_sym, spc_size = '', '', 0
# format min/max depth
try:
dmin, dmax = depth.split()
except:
print('you must provide -d in this format: -d dmin dmax')
print('could not parse {}, defaulting to plotting all depths'.format(depth))
dmin, dmax = -1, -1
# format timescale, min/max time
if timescale:
try:
timescale, amin, amax = timescale.split()
pltTime = True
except:
print(
'you must provide -ts in this format: -ts timescale minimum_age maximum_age')
print(
'could not parse {}, defaulting to using no timescale'.format(timescale))
timescale, amin, amax = None, -1, -1
pltTime = False
else:
timescale, amin, amax = None, -1, -1
pltTime = False
# format norm and wt_file
if norm and not isinstance(norm, bool):
wt_file = norm
norm = True
else:
norm = False
wt_file = ''
# format list of protcols and step
try:
method, step = meth.split()
except:
print(
'To use the -LP flag you must provide both the protocol and the step in this format:\n-LP [AF,T,ARM,IRM, X] step [in mT,C,mT,mT, mass/vol] to plot')
print('Defaulting to using no protocol')
method, step = 'LT-NO', 0
# list of varnames
#['f', 'fsum', 'fwig', 'fsa', 'fa', 'fsp', 'fres', 'fmt', 'LP', 'n', 'd', 'ts', 'WD', 'L', 'S', 'D', 'I', 'M', 'log', 'ds', 'sym' ]
#meas_file, sum_file, wig_file, samp_file, age_file, spc_file, res_file, fmt, meth, norm, depth, timescale, dir_path, pltLine, pltSus, pltDec, pltInc, pltMag, logit, depth_scale, symbol
fig, figname = ipmag.core_depthplot(input_dir, meas_file, spc_file, samp_file, age_file, sum_file, wt_file, depth_scale, dmin, dmax, sym, size,
spc_sym, spc_size, method, step, fmt, pltDec, pltInc, pltMag, pltLine, pltSus, logit, pltTime, timescale, amin, amax, norm, data_model_num)
if not pmagplotlib.isServer:
figname = figname.replace(':', '_')
if fig and save:
print('-I- Created plot: {}'.format(figname))
plt.savefig(figname)
return
app = wx.App(redirect=False)
if not fig:
pw.simple_warning(
'No plot was able to be created with the data you provided.\nMake sure you have given all the required information and try again')
return False
dpi = fig.get_dpi()
pixel_width = dpi * fig.get_figwidth()
pixel_height = dpi * fig.get_figheight()
figname = os.path.join(dir_path, figname)
plot_frame = pmag_menu_dialogs.PlotFrame((int(pixel_width), int(pixel_height + 50)),
fig, figname, standalone=True)
app.MainLoop()
def main():
"""
NAME
ani_depthplot.py
DESCRIPTION
plots tau, V3_inc, V1_dec, P and chi versus core_depth
SYNTAX
ani_depthplot.py [command line optins]
# or, for Anaconda users:
ani_depthplot_anaconda [command line options]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic (MagIC 2 only)
-fb FILE: specify input measurements format file from magic
-fsa FILE: specify input sample format file from magic
-fsp FILE: specify input specimen file (MagIC 3 only)
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf (core depth)
-sav save plot without review
-fmt specfiy format for figures - default is svg
DEFAULTS:
Anisotropy file: specimens.txt
Bulk susceptibility file: measurements.txt
Samples file: samples.txt
"""
args = sys.argv
if '-h' in args:
print(main.__doc__)
sys.exit()
dataframe = extractor.command_line_dataframe([['f', False, 'rmag_anisotropy.txt'],
['fb', False, 'magic_measurements.txt'],
['fsa', False, 'er_samples.txt'],
['fa', False, None], ['fsum', False, None],
['fmt', False, 'svg'], ['ds', False, 'mbsf'],
['d', False, '-1 -1'], ['sav', False, False],
['WD', False, '.' ], ['DM', False, 3],
['fsp', False, 'specimens.txt']])
#args = sys.argv
checked_args = extractor.extract_and_check_args(args, dataframe)
ani_file, meas_file, samp_file, age_file, sum_file, fmt, depth_scale, depth, save_quietly, dir_path, data_model, spec_file = extractor.get_vars(['f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD', 'DM', 'fsp'], checked_args)
# format min/max depth
try:
dmin, dmax = depth.split()
dmin, dmax = float(dmin), float(dmax)
except:
print('you must provide depth in this format: -d dmin dmax')
print('could not parse "{}", defaulting to plotting all depths'.format('-d ' + str(depth)))
dmin, dmax = -1, -1
if depth_scale:
if depth_scale not in ['age', 'mbsf', 'mcd']:
print('-W- Unrecognized option "{}" provided for depth scale.\n Options for depth scale are mbsf (meters below sea floor) or mcd (meters composite depth).\n Alternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\n Using default "mbsf"'.format(depth_scale))
depth_scale = 'sample_core_depth'
if age_file:
depth_scale = 'age'
elif 'mbsf' in depth_scale:
depth_scale = 'sample_core_depth'
elif 'mcd' in depth_scale:
depth_scale = 'sample_composite_depth'
data_model = int(float(data_model))
# MagIC 2
if data_model == 2:
fig, figname = ipmag.ani_depthplot2(ani_file, meas_file, samp_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
# MagIC 3
else:
if meas_file == "magic_measurements.txt":
meas_file = 'measurements.txt'
if samp_file in ['er_samples.txt', 'pmag_samples.txt']:
samp_file = "samples.txt"
site_file = 'sites.txt'
fig, fignames = ipmag.ani_depthplot(spec_file, samp_file, meas_file, site_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
figname = fignames[0]
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
plt.savefig(figname)
plt.clf()
print('Saved file: {}'.format(figname))
return False
app = wx.App(redirect=False)
if not fig:
pw.simple_warning('No plot was able to be created with the data you provided.\nMake sure you have given all the required information and try again')
return False
dpi = fig.get_dpi()
pixel_width = dpi * fig.get_figwidth()
pixel_height = dpi * fig.get_figheight()
figname = os.path.join(dir_path, figname)
plot_frame = pmag_menu_dialogs.PlotFrame((int(pixel_width), int(pixel_height + 50)),
fig, figname, standalone=True)
app.MainLoop()
def make_grid_frame(self, event):
"""
Create a GridFrame for data type of the button that was clicked
"""
if self.grid_frame:
print('-I- You already have a grid frame open')
pw.simple_warning("You already have a grid open")
return
try:
grid_type = event.GetButtonObj().Name[:-4] # remove '_btn'
except AttributeError:
grid_type = self.FindWindowById(
event.Id).Name[:-4] # remove ('_btn')
wait = wx.BusyInfo('Making {} grid, please wait...'.format(grid_type))
wx.Yield()
# propagate site lat/lon info into locations if necessary
if grid_type == 'locations' and 'sites' in self.contribution.tables:
self.contribution.get_min_max_lat_lon()
self.contribution.propagate_cols_up(
['lithologies', 'geologic_classes'], 'locations', 'sites')
# propagate lithologies/type/class information from sites to samples/specimens
if grid_type in ['specimens', 'samples']:
self.contribution.propagate_lithology_cols()
# propagate average lat/lon info from samples table if
# available in samples and missing in sites
if grid_type == 'sites':
self.contribution.propagate_average_up(
cols=['lat', 'lon', 'height'],
target_df_name='sites',
source_df_name='samples')
self.contribution.propagate_lithology_cols()
# hide mainframe
self.on_open_grid_frame()
# choose appropriate size for grid
if grid_type == 'measurements':
huge = True
else:
huge = False
# make grid frame
self.grid_frame = grid_frame.GridFrame(self.contribution,
self.WD,
grid_type,
grid_type,
self.panel,
huge=huge)
row_string = ""
# paint validations if appropriate
if self.validation_mode:
if grid_type in self.validation_mode:
if grid_type == 'measurements':
skip_cell_render = True
else:
skip_cell_render = False
self.grid_frame.toggle_help(None, "open")
row_problems = self.failing_items[grid_type]["rows"]
missing_columns = self.failing_items[grid_type][
"missing_columns"]
missing_groups = self.failing_items[grid_type][
"missing_groups"]
#all_cols = row_problems.columns
#col_nums = range(len(all_cols))
#col_pos = dict(zip(all_cols, col_nums))
if len(row_problems):
row_string = "Columns and rows with problem data have been highlighted in blue.\n"
if not skip_cell_render:
row_string += "Cells with problem data are highlighted according to the type of problem.\nRed: incorrect data\n"
row_string += "For full error messages, see {}.".format(
grid_type + "_errors.txt")
for row in row_problems['num']:
self.grid_frame.grid.paint_invalid_row(row)
mask = row_problems["num"] == row
items = row_problems[mask]
cols = items.dropna(how="all",
axis=1).drop(["num", "issues"],
axis=1)
for col in cols:
pre, col_name = val_up3.extract_col_name(col)
col_ind = self.grid_frame.grid.col_labels.index(
col_name)
self.grid_frame.grid.paint_invalid_cell(
row, col_ind, skip_cell=skip_cell_render)
current_label = self.grid_frame.msg_text.GetLabel()
if len(missing_columns):
col_string = "You are missing the following required columns: {}\n\n".format(
", ".join(missing_columns))
else:
col_string = ""
if len(missing_groups):
group_string = "You must have at least one column from each of the following groups: {}\n\n".format(
", ".join(missing_groups))
else:
group_string = ""
#
add_text = """{}{}{}""".format(col_string, group_string,
row_string)
self.grid_frame.msg_text.SetLabel(add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
self.grid_frame.do_fit(None)
del wait
def on_okButton(self, event):
meas_files = []
spec_files = []
samp_files = []
site_files = []
loc_files = []
for i in range(self.max_files):
# read directory path
dirpath = self.dir_paths[i].GetValue()
if dirpath != "":
dir_name = os.path.realpath(dirpath)
#dir_name = str(dirpath.split("/")[-1])
else:
continue
# get location
location_name = self.file_locations[i].GetValue()
# get sample-specimen naming convention
samp_con = str(self.naming_con_boxes[i].GetValue())
samp_chars = str(self.naming_con_char[i].GetValue())
samp_chars = samp_chars.strip('"').strip("'")
if samp_con == "character delimited" and not samp_chars:
pw.simple_warning("To delimit samples by character, you must provide the delimiter, (eg. \"-\" or \"_\")!")
return
# get site-sample naming convention
site_con = str(self.site_name_conventions[i].GetValue())
site_chars = str(self.site_name_chars[i].GetValue())
site_chars = site_chars.strip('"').strip("'")
if site_con == "character delimited" and not site_chars:
pw.simple_warning("To delimit sites by character, you must provide the delimiter, (eg. \"-\" or \"_\")!")
return
# name output files
if self.data_model_num == 2:
meas_out = "magic_measurements_{}.txt".format(i)
spec_out = "er_specimens_{}.txt".format(i)
samp_out = "er_samples_{}.txt".format(i)
site_out = "er_sites_{}.txt".format(i)
loc_out = "er_locations_{}.txt".format(i)
else:
meas_out = "measurements_{}.txt".format(i)
spec_out = "specimens_{}.txt".format(i)
samp_out = "samples_{}.txt".format(i)
site_out = "sites_{}.txt".format(i)
loc_out = "locations_{}.txt".format(i)
# do conversion
convert.livdb(dir_name, self.WD, meas_out, spec_out,
samp_out, site_out, loc_out,
samp_con, samp_chars, site_con,
site_chars, location_name)
meas_files.append(meas_out)
spec_files.append(spec_out)
samp_files.append(samp_out)
site_files.append(site_out)
loc_files.append(loc_out)
if self.data_model_num == 2:
res = ipmag.combine_magic(meas_files, "magic_measurements.txt", 2)
ipmag.combine_magic(spec_files, "er_specimens.txt", 2)
else:
res = ipmag.combine_magic(meas_files, "measurements.txt", 3)
ipmag.combine_magic(spec_files, "specimens.txt", 3)
ipmag.combine_magic(samp_files, "samples.txt", 3)
ipmag.combine_magic(site_files, "sites.txt", 3)
ipmag.combine_magic(loc_files, "locations.txt", 3)
pmag.remove_files(meas_files)
pmag.remove_files(spec_files)
pmag.remove_files(samp_files)
pmag.remove_files(site_files)
pmag.remove_files(loc_files)
if res:
self.after_convert_dia()
else:
pw.simple_warning("Something when wrong with one or more of your files.\nSee Terminal/Command Prompt output for more details")
