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))
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
"""
self.grid_frame.msg_text.SetLabel(current_label + add_text)
#self.on_finish_change_dir(self.change_dir_dialog)
del wait
def onImport(self, event):
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:
if self.grid_type == 'age':
import_type = 'age'
parent_type = None
filename = openFileDialog.GetPath()
file_type = self.er_magic.get_age_info(filename)
import_type = file_type.split('_')[1][:-1]
elif self.grid_type == 'result':
import_type = 'result'
parent_type = None
try:
filename = openFileDialog.GetPath()
self.er_magic.get_results_info(filename)
except Exception as ex:
print '-W- ', ex
print '-W- Could not read file:\n{}\nFile may be corrupted, or may not be a results format file.'.format(filename)
pw.simple_warning('Could not read file:\n{}\nFile may be corrupted, or may not be a results format file.'.format(filename))
return
else:
parent_ind = self.er_magic.ancestry.index(self.grid_type)
parent_type = self.er_magic.ancestry[parent_ind+1]
# get filename and file data
filename = openFileDialog.GetPath()
import_type = self.er_magic.get_magic_info(self.grid_type, parent_type,
filename=filename, sort_by_file_type=True)
# add any additional headers to the grid, while preserving all old headers
current_headers = self.grid_headers[self.grid_type]['er'][0]
self.er_magic.init_actual_headers()
er_headers = list(set(self.er_magic.headers[self.grid_type]['er'][0]).union(current_headers))
self.er_magic.headers[self.grid_type]['er'][0] = er_headers
#include_pmag = self.pmag_checkbox.cb.IsChecked()
include_pmag = True
if include_pmag:
pmag_headers = self.er_magic.headers[self.grid_type]['pmag'][0]
headers = set(er_headers).union(pmag_headers)
else:
headers = er_headers
for head in sorted(list(headers)):
if head not in self.grid.col_labels:
self.grid.add_col(head)
# add age data
if import_type == 'age' and self.grid_type == 'age':
self.grid_builder.add_age_data_to_grid()
self.grid.size_grid()
self.main_sizer.Fit(self)
elif import_type == self.grid_type:
self.grid_builder.add_data_to_grid(self.grid, import_type)
self.grid.size_grid()
self.main_sizer.Fit(self)
# if imported data will not show up in current grid,
# warn user
else:
pw.simple_warning('You have imported a {} type file.\nYou\'ll need to open up your {} grid to see this data'.format(import_type, import_type))
def onDeleteRow(self, event, data_type):
"""
On button click, remove relevant object from both the data model and the grid.
"""
ancestry = self.er_magic_data.ancestry
child_type = ancestry[ancestry.index(data_type) - 1]
names = [self.grid.GetCellValue(row, 0) for row in self.selected_rows]
if data_type == 'site':
how_to_fix = 'Make sure to select a new site for each orphaned sample in the next step'
else:
how_to_fix = 'Go back a step and select a new {} for each orphaned {}'.format(data_type, child_type)
orphans = []
for name in names:
row = self.grid.row_labels.index(name)
orphan = self.er_magic_data.delete_methods[data_type](name)
if orphan:
orphans.extend(orphan)
self.grid.remove_row(row)
if orphans:
orphan_names = self.er_magic_data.make_name_list(orphans)
pw.simple_warning('You have deleted:\n\n {}\n\nthe parent(s) of {}(s):\n\n {}\n\n{}'.format(', '.join(names), child_type, ', '.join(orphan_names), how_to_fix))
self.selected_rows = set()
# update grid and data model
self.update_grid(self.grid)#, grids[grid_name])
self.grid.Refresh()
def on_er_data(self, event):
if not os.path.isfile(os.path.join(self.WD, 'magic_measurements.txt')):
import 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)
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()
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_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', list(items), [])
dia.Centre()
result2 = dia.ShowModal()
else:
groups = self.dm['group'].unique()
dia = pw.HeaderDialog(self, 'groups to add', list(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
er_items = [head for head in self.grid_headers[self.grid_type]['er'][2] if head not in col_labels]
er_items = builder.remove_list_headers(er_items)
#include_pmag = self.pmag_checkbox.cb.IsChecked()
include_pmag = True
if include_pmag or self.grid_type == 'result':
pmag_headers = sorted(list(set(self.grid_headers[self.grid_type]['pmag'][2]).union(self.grid_headers[self.grid_type]['pmag'][1])))
pmag_items = [head for head in pmag_headers if head not in er_items and head not in col_labels]
#pmag_items = [head for head in self.grid_headers[self.grid_type]['pmag'][2] if head not in er_items and head not in col_labels]
pmag_items = builder.remove_list_headers(pmag_items)
else:
pmag_items = []
dia = pw.HeaderDialog(self, 'columns to add', er_items, pmag_items)
result = dia.ShowModal()
new_headers = []
if result == 5100:
new_headers = dia.text_list
if not new_headers:
return
for name in new_headers:
if name:
if name not in self.grid.col_labels:
col_number = self.grid.add_col(name)
# add to appropriate headers list
if name in er_items:
self.grid_headers[self.grid_type]['er'][0].append(str(name))
if name in pmag_items:
self.grid_headers[self.grid_type]['pmag'][0].append(str(name))
import controlled_vocabularies as vocabulary
from controlled_vocabularies import vocabularies as vocab
if name in vocabulary.possible_vocabularies:
self.drop_down_menu.add_drop_down(col_number, name)
else:
pw.simple_warning('You are already using column header: {}'.format(name))
# 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.main_sizer.Fit(self)
#
self.grid.changes = set(range(self.grid.GetNumberRows()))
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_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', list(items), [])
dia.Centre()
result2 = dia.ShowModal()
else:
groups = self.dm['group'].unique()
dia = pw.HeaderDialog(self, 'groups to add', list(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 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('**')
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_add_cols(self, event):
"""
Show simple dialog that allows user to add a new column name
"""
col_labels = self.grid.col_labels
# do not list headers that are already column labels in the grid
er_items = [head for head in self.grid_headers[self.grid_type]['er'][2] if head not in col_labels]
# remove unneeded headers
er_items = builder.remove_list_headers(er_items)
pmag_headers = sorted(list(set(self.grid_headers[self.grid_type]['pmag'][2]).union(self.grid_headers[self.grid_type]['pmag'][1])))
# do not list headers that are already column labels in the grid
# make sure that pmag_specific columns are marked with '++'
to_add = [i + '++' for i in self.er_magic.double if i in pmag_headers and i + '++' not in col_labels]
pmag_headers.extend(to_add)
pmag_items = [head for head in pmag_headers if head not in er_items and head not in col_labels]
# remove unneeded headers
pmag_items = sorted(builder.remove_list_headers(pmag_items))
dia = pw.HeaderDialog(self, 'columns to add', er_items, pmag_items)
dia.Centre()
result = dia.ShowModal()
new_headers = []
if result == 5100:
new_headers = dia.text_list
if not new_headers:
return
errors = self.add_new_grid_headers(new_headers, er_items, pmag_items)
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 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 remove_col_label(self, event):#, include_pmag=True):
"""
check to see if column is required
if it is not, delete it from grid
"""
er_possible_headers = self.grid_headers[self.grid_type]['er'][2]
pmag_possible_headers = self.grid_headers[self.grid_type]['pmag'][2]
er_actual_headers = self.grid_headers[self.grid_type]['er'][0]
pmag_actual_headers = self.grid_headers[self.grid_type]['pmag'][0]
col = event.GetCol()
label = self.grid.GetColLabelValue(col)
if '**' in label:
label = label.strip('**')
if label in self.grid_headers[self.grid_type]['er'][1]:
pw.simple_warning("That header is required, and cannot be removed")
return False
#elif include_pmag and label in self.grid_headers[self.grid_type]['pmag'][1]:
# 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)
#if label in er_possible_headers:
try:
print 'removing {} from er_actual_headers'.format(label)
er_actual_headers.remove(label)
except ValueError:
pass
#if label in pmag_possible_headers:
try:
pmag_actual_headers.remove(label)
except ValueError:
pass
# causes resize on each column header delete
# can leave this out if we want.....
self.main_sizer.Fit(self)
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]
OPTIONS
-h prints help message and quits
-f FILE: specify input rmag_anisotropy format file from magic
-fb FILE: specify input magic_measurements format file from magic
-fsa FILE: specify input er_samples format file from magic
-fsum FILE : specify input LIMS database (IODP) core summary csv file
to print the core names, set lab to 1
-fa FILE: specify input er_ages format file from magic
-d min max [in m] depth range to plot
-ds [mcd,mbsf], specify depth scale, default is mbsf
-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, '.' ]])
#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 = extractor.get_vars(['f', 'fb', 'fsa', 'fa', 'fsum', 'fmt', 'ds', 'd', 'sav', 'WD'], 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 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'
else:
print 'Warning: Unrecognized option "{}" provided for depth scale.\nOptions for depth scale are mbsf -- meters below sea floor -- or mcd -- meters composite depth.\nAlternatively, if you provide an age file the depth scale will be automatically set to plot by age instead.\nUsing default "mbsf"'.format(depth_scale)
depth_scale = 'sample_composite_depth'
fig, figname = ipmag.aniso_depthplot(ani_file, meas_file, samp_file, age_file, sum_file, fmt, dmin, dmax, depth_scale, dir_path)
if save_quietly:
if dir_path == '.':
dir_path = os.getcwd()
print 'Saved file: {} in folder: {}'.format(figname, dir_path)
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)
app.MainLoop()
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 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, ''], ['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, '.']])
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 = 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'], 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)
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)
app.MainLoop()
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
