def choosechannels(data, channel1, channel2):
# Obtain the data field ids for the data file (i.e. the various channels within the file)
ids = gwy.gwy_app_data_browser_get_data_ids(data)
# Make an empty array for the chosen channels to be saved into
chosen_ids = []
# Find channels with the title ZSensor, if these do not exist, find channels with the title Height
chosen_ids = gwy.gwy_app_data_browser_find_data_by_title(data, channel1)
if not chosen_ids:
chosen_ids = gwy.gwy_app_data_browser_find_data_by_title(data, channel2)
else:
chosen_ids = chosen_ids
# Save out chosen_ids as a list of the channel ids for ZSensor or height if ZSensor doesnt exist
return chosen_ids
def __init__(self, m_file, **kwargs):
self.surface = None
Data.__init__(self, m_file, **kwargs)
self.container = gwy.gwy_file_load(self.m_file, gwy.RUN_NONINTERACTIVE)
gwy.gwy_app_data_browser_add(self.container)
self.channel_id = gwy.gwy_app_data_browser_find_data_by_title(
self.container, "*SE*"
)[0]
gwy.gwy_app_data_browser_select_data_field(self.container, self.channel_id)
self.extract_meta(gwyddion.get_meta_ids(self.container)[0])
def find_channel(self, match_list):
"""Finds the right data channel within a Gwyddion container.
Args:
container: Gwyddion container with several data channels.
match_list (list): Names which will be searched. e.g. topography
Returns:
chn_ids (list): List of channel IDs.
"""
self.ch_ids = []
for self._data_title in match_list:
self._match_ch = gwy.gwy_app_data_browser_find_data_by_title(
self.container, self._data_title)
self.ch_ids.extend(self._match_ch)
return self.ch_ids
def return_match_ch(self, pattern, channels):
"""Returns topography channels
Args:
pattern: Pattern list, which identifies the desired channel.
channels: List of channels.
Returns:
ch (list): Channel ids.
"""
for pat in pattern:
self.topo_ch = [ch for ch in channels if re.search(pat, ch)]
if len(self.topo_ch) > 0:
break
return [
gwy.gwy_app_data_browser_find_data_by_title(self.container, ch)
for ch in self.topo_ch
]
def gwybas(filename):
#add the gwyddion folders to the path, making sure they can be found
import sys
sys.path.append('C:\Program Files (x86)\Gwyddion\\bin')
sys.path.append('C:\Program Files (x86)\Gwyddion\share\gwyddion\pygwy')
#import gwyddion
import gwy
import gwyutils
#load the file and add to data browser
c = gwy.gwy_file_load(filename, gwy.RUN_IMMEDIATE)
gwy.gwy_app_data_browser_add(c)
#Set the right settings for the align_rows command
settings = gwy.gwy_app_settings_get()
settings['/module/linematch/direction'] = int(gwy.ORIENTATION_HORIZONTAL)
settings['/module/linematch/do_extract'] = False
settings['/module/linematch/do_plot'] = False
settings[
'/module/linematch/method'] = 0 # 0: poly, 1: median, 2: median of diff,3: modus,4: matching, 5: trimemd mean, 6: trimmed mean of diff
settings['/module/linematch/masking'] = 2
settings['/module/linematch/max_degree'] = 3 #Order of polynominal
settings['/module/linematch/trim_fraction'] = 0.05
#print the datafield ID's corresponding to the different channels of the AFM, such as height, phase and error, usually the first one (0) is the height
# print gwy.gwy_app_data_browser_get_data_ids(c)
#itterate over the different datafield ID's/AFM channels, and do processing on them
for datafield_id in gwy.gwy_app_data_browser_get_data_ids(c):
# datafield = c['/%d/data' % datafield_id]
#set the color range to automatic with tials cut off (corresponding to number 2)
c['/%d/base/range-type' % datafield_id] = 2
#select the datafield_ID/AFM channel to process
gwy.gwy_app_data_browser_select_data_field(c, datafield_id)
#level the plane
gwy.gwy_process_func_run("level", c, gwy.RUN_IMMEDIATE)
#align the rows, with settings chosen above line 19-25
gwy.gwy_process_func_run("align_rows", c, gwy.RUN_IMMEDIATE)
#remove scars a couple of times (button bashing)
gwy.gwy_process_func_run("scars_remove", c, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("scars_remove", c, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("scars_remove", c, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("scars_remove", c, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("scars_remove", c, gwy.RUN_IMMEDIATE)
#fix lowest point to zero
gwy.gwy_process_func_run('fix_zero', c, gwy.RUN_IMMEDIATE)
#define new file names, I chose to simply add the wanted extention to the original filename
newname = filename + '.gwy'
newname2 = filename + '.jpg'
#find the ID/Channel corresponding to the height, of this one a JPG will be created, .gwy will contain all channels
ids = gwy.gwy_app_data_browser_find_data_by_title(c, 'Height')
gwy.gwy_app_data_browser_select_data_field(c, ids[0])
gwy.gwy_file_save(c, newname, gwy.RUN_NONINTERACTIVE)
gwy.gwy_file_save(c, newname2, gwy.RUN_NONINTERACTIVE)
#remove the current container, makes room for the next file
gwy.gwy_app_data_browser_remove(c)
if file_name[-4:] == '.spm':
full_file_name = directory + file_name
try:
spm_file_list.append(full_file_name)
except NameError:
spm_file_list = [full_file_name]
for image in spm_file_list:
#Load the image and make it current in the gwyddion data browser
gwy_rawdata = gwy.gwy_file_load(image, gwy.RUN_NONINTERACTIVE)
gwy.gwy_app_data_browser_add(gwy_rawdata)
#Find the id locators for the height
height_ids = gwy.gwy_app_data_browser_find_data_by_title(
gwy_rawdata, 'Height')
#Get the settings for each function from the saved settings file (~/.gwyddion/settings)
s = gwy.gwy_app_settings_get()
configureGwySettings(s)
#Process both trace and retrace
for i in height_ids:
###
### CORRECTING THE DATA WITH GWYDDION FUNCTIONS
### HAVE INCREDIBLY UNPLEASANT LOOKING EDITING OF SETTINGS TO DO FOR EACH FUNCTION
### PROBABLY A NEATER WAY TO DO THIS BUT CBA TO LOOK FOR IT NOW
### COPIED THE SETTINGS FROM THE ~/.gwyddion/settings file
###