def import_file(self, evt=None, file_path=None):
if file_path is None:
file_path = FileDialogs.open_file_dialog("Open File", "*.csv")
if file_path is not None:
# read in the comma-delimited import file
f = open(file_path, 'r')
lines = f.readlines()
f.close()
type = lines[0].split(",")[1]
if type.lower() == "scans":
print("Type Scans:", type)
self.rb.SetSelection(1)
self.my_grid.EvtDriftType(1)
else:
print("Type Time:", type)
self.rb.SetSelection(0)
self.my_grid.EvtDriftType(0)
data = np.genfromtxt(file_path,
delimiter=",",
skip_header=2,
dtype=np.str)
print("Data:", data)
self.my_grid.load_data(data)
def auto(self, evt, file_path=None, filtered_lines=None):
if file_path is None and (filtered_lines is None or len(filtered_lines) <= 2):
file_path = FileDialogs.open_file_dialog("Open File", "*.csv")
filtered_lines = []
if file_path is not None:
# read in the comma-delimited import file
f = open(file_path, 'r')
lines = f.readlines()
f.close()
# strip lines beginning with # so can comment out lines
# strip blank lines
for line in lines:
if line.strip() is '' or line[0] is '#':
continue
filtered_lines.append(line)
if filtered_lines is not None and len(filtered_lines) > 2: # i.e. more than just hopefully the two header lines
t = threading.Thread(target=data_importer.auto_from_wizard, args=(filtered_lines, self.exedir))
t.start()
# gauge=ImporterProgressGauge.ProgressDialog()
# gauge.progress_dialog(self,"Importing raw file(s)","Importing file %s of %s, please wait..." % (1, len(filtered_lines) - 2),len(filtered_lines) - 2)
ImporterProgressGauge.progress_dialog(self, "Importing raw file(s)",
"Importing file %s of %s, please wait..." % (
1, len(filtered_lines) - 2), len(filtered_lines) - 2)
def on_load_common_masses(self, e):
cmfilename = FileDialogs.open_file_dialog(
"Open Common Masses File",
file_types="*.csv*",
default=self.config.masstablefile)
if cmfilename is not None:
self.load_common_masses(cmfilename)
def on_save_fig(self, e=None):
path = FileDialogs.save_file_dialog()
base, ext = os.path.splitext(path)
#self.init()
#self.save_fig(base,ext)
for i in range(0, len(self.datalist)):
self.on_next(None)
self.save_fig(base, ext)
def on_save_common_masses(self, e):
outdata = self.commonmassespanel.list.get_list()
cmfilename = FileDialogs.save_file_dialog("Save Common Masses File",
"*.csv*",
self.config.masstablefile)
if cmfilename is not None:
np.savetxt(cmfilename, outdata, delimiter=",", fmt="%s")
print("Saving Common Masses to:", cmfilename)
def get_folder_path(self, evt):
'''
Get path to folder and place in txtctrl
'''
path = FileDialogs.open_dir_dialog()
if path != None:
self.folder_path.SetValue(path)
self.my_tree.populate_tree()
def auto(self, evt=None, file_path=None):
if file_path is None:
file_path = FileDialogs.save_file_dialog("Save File As", "*.hdf5")
filtered_lines = []
if file_path is not None:
cols, data = self.my_grid.get_data()
meta_data_importer.auto_from_wizard(data, file_path,
self.rb.GetSelection())
def on_save_fig_dialog(self, evt):
"""
Open a save figure dialog for specified plot.
:param evt: wx.Event (unused)
:return: None
"""
path = FileDialogs.save_file_dialog()
if path is not None:
self.save_figure(path)
def on_load_conf_file(self, e=None):
"""
Opens a file dialog and then imports a new _conf.dat config file
:param e: unused space for event
:return: None
"""
cfilename = FileDialogs.open_file_dialog("Open Configuration File (_conf.dat)", file_types="*.*")
if cfilename is not None:
self.import_config(cfilename)
pass
def on_import_masses(self, e):
"""
Opens a dialog to import mass list files.
:param e: Unused event
:return: None
"""
mfilename = FileDialogs.open_file_dialog(
"Open Text File with List of Mass Defects", file_types="*.*")
if mfilename is not None:
importmass = np.loadtxt(mfilename)
self.masslistbox.list.populate(importmass)
def on_import_masses(self, e):
"""
Opens a dialog to import mass list files.
:param e: Unused event
:return: None
"""
mfilename = FileDialogs.open_file_dialog("Open Mass File (mfile)",
file_types="*.*")
if mfilename is not None:
importmass = np.loadtxt(mfilename)
if importmass[0] > 0:
self.masslistbox.list.populate(importmass)
def on_import_oligos(self, e):
"""
Open a file dialog to import oligomer files.
:param e: Unused event
:return: None
"""
# TODO: This fails when the output ofile isn't square (some are unnamed and other are named)
ofilename = FileDialogs.open_file_dialog("Open Oligomer File (ofile)",
file_types="*.*")
if ofilename is not None:
importolig = np.genfromtxt(ofilename, dtype='str')
if np.shape(importolig) == (5, ) or np.shape(importolig) == (4, ):
importolig = [importolig]
self.oligomerlistbox.list.populate(importolig)
def on_write_dialog(self, evt):
"""
Open a save figure dialog for specified plot.
:param evt: wx.Event (unused)
:return: None
"""
if self.data is not None:
path = FileDialogs.save_file_dialog()
if path is not None:
self.write_data(path)
else:
print(
"Data object empty. Plot likely unsupported for text file output."
)
def export_file(self, evt):
'''
Export import file for later import
'''
file_path = FileDialogs.save_file_dialog(message="Save Import CSV File", file_types="CSV (*.csv)|*.csv")
max_index = self.my_grid.next_free_row()
if file_path != None and max_index > 0:
if file_path[-17:] != '_ionMS_import.csv' and file_path[-4:] != '.csv':
file_path += '_ionMS_import.csv'
f = open(file_path, 'w')
# get im type
if self.rb.GetSelection() == 0:
f.writelines('ionMS import wizard,Linear,\n')
elif self.rb.GetSelection() == 2:
f.writelines("ionMS import wizard,MS,\n")
elif self.rb.GetSelection() == 3:
f.writelines("ionMS import wizard,MS Times,\n")
else:
f.writelines('ionMS import wizard,T-wave,\n')
index = -1
while True:
# get column labels
cols = self.my_grid.column_labels()
index += 1
if index == max_index:
break
if index == 0:
# write column labels
tmp = ''
for c in cols:
tmp += '%s,' % cols[c]
f.writelines(tmp[:-1] + '\n')
# write out user import list
tmp = ''
for c in cols:
tmp += '%s,' % self.my_grid.GetCellValue(index, c)
f.writelines(tmp[:-1] + '\n')
# don't forget to close the file
f.close()
return file_path # + '_ionMS_import.csv'
def on_import(self, e):
"""
Open a file dialog and import a N x 3 (MS) or N x 5 (IMMS) array of manual assignment.
Add the array to the listctrl.
:param e: Unused event
:return: None
"""
import_file_name = FileDialogs.open_file_dialog("Open File",
file_types="*.*")
if import_file_name is not None:
importtrunc = np.loadtxt(import_file_name)
if self.config.imflag == 0:
if importtrunc.shape == (3, ):
importtrunc = [importtrunc]
if len(importtrunc[0]) == 3:
self.masslistbox.list.populate(importtrunc)
# print importtrunc
else:
if importtrunc.shape == (5, ):
importtrunc = [importtrunc]
if len(importtrunc[0]) == 5:
self.masslistbox.list.populate(importtrunc)
def export_file(self, evt):
'''
Export import file for later import
'''
file_path = FileDialogs.save_file_dialog(
message="Save Import CSV File", file_types="CSV (*.csv)|*.csv")
max_index = self.my_grid.next_free_row()
if file_path != None and max_index > 0:
if file_path[-17:] != '_import.csv' and file_path[-4:] != '.csv':
file_path += '_import.csv'
cols, data = self.my_grid.get_data()
f = open(file_path, 'w')
# Write Type at the Top
if self.rb.GetSelection() == 0:
f.writelines('MetaUniDec Import Wizard,Time,\n')
elif self.rb.GetSelection() == 1:
f.writelines("MetaUniDec Import Wizard,Scans,\n")
# Write Column Values
tmp = ''
for c in cols:
tmp += '%s,' % cols[c]
f.writelines(tmp[:-1] + '\n')
# Write Data
for i, a in enumerate(data):
for j, l in enumerate(a):
f.write(str(l) + ",")
f.write('\n')
# close the file
f.close()
return file_path
def on_batch_chrom_dirs(self, e=None):
paths = FileDialogs.open_multiple_dir_dialog(
message="Choose Waters or Agilent files to batch process.",
default=None)
print("Batch Run Directories:", paths)
self.batch_run(paths)
def on_open_dir(self, e=None):
dirname = FileDialogs.open_single_dir_dialog("Choose a raw file", '')
print("Opening Directory: ", dirname)
if dirname is not None:
if os.path.splitext(dirname)[1] in chrom_file_exts:
self.open_file(dirname)
def on_batch_chrom1(self, e=None):
paths = FileDialogs.open_multiple_files_dialog(
message="Choose files to batch process.", file_type="*.*")
print("Batch Run:", paths)
self.batch_run(paths)
