def get_gaussian_sigma():
"""
Convenience function that gets the gaussian sigma value from the filters toolbox setting.
Size (FWHM) relates to sigma as FWHM = 2*sqrt(2*ln(2)) * sigma.
Returns
-------
sigma: float
Standard deviation of gaussian kernel.
"""
settings = gwy.gwy_app_settings_get()
# get sigma from settings, ie. vlaue last used in toolbox->filters
size = settings["/module/filter/gauss_size"]
# size (FWHM) relates to sigma as FWHM = 2*sqrt(2*ln(2)) * sigma
return size / (2.0 * math.sqrt(2.0 * math.log(2.0)))
def set_settings(self):
"""Sets the setting which are supplied by the user editable config file."""
self.settings = gwy.gwy_app_settings_get()
self.settings["/module/linematch/direction"] = int(
gwy.ORIENTATION_HORIZONTAL)
self.settings["/module/linematch/do_extract"] = config.do_extract
self.settings["/module/linematch/do_plot"] = config.do_plot
self.settings["/module/linematch/method"] = config.method
self.settings["/module/linematch/masking"] = config.masking
self.settings["/module/linematch/max_degree"] = config.max_degree
self.settings["/module/median-bg/radius"] = config.radius
self.settings["/module/median-bg/do_extract"] = config.do_extract
self.settings["/module/rotate/angle"] = config.angle
self.settings["/module/rotate/create_mask"] = config.create_mask
self.settings["/module/rotate/interp"] = config.rotate_interp
self.settings["/module/rotate/resize"] = config.resize
self.settings["/module/rotate/show_grid"] = config.show_grid
self.settings["/module/scale/interp"] = config.scale_interp
self.settings["/module/scale/proportional"] = config.proportional
self.settings["/module/scale/aspectratio"] = config.aspectratio
self.settings["/module/asciiexport/add-comment"] = config.add_comment
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)
import gwyutils, gwy, gc
from os import listdir, mkdir, getcwd
from os.path import isfile, join
cwd = '/home/june/pygwy/cont'
Files_To_Open = [ f for f in listdir(cwd) if isfile(join(cwd,f)) ]
#mkdir(join(cwd,'Processed'))
filename_save = getcwd().split('/')[-1]
# Export PNG with scalebar
s = gwy.gwy_app_settings_get()
s['/module/pixmap/title_type'] = 0
s['/module/pixmap/ztype'] = 0
s['/module/pixmap/xytype'] = 0
s['/module/pixmap/draw_maskkey'] = False
# ... (*lots* of possible settings, see ~/.gwyddion/settings)
#Load first file to use as Merged file
Cont_Dest = gwy.gwy_file_load(join(cwd,Files_To_Open[0]), RUN_NONINTERACTIVE)
gwy.gwy_app_data_browser_add(Cont_Dest)
#Make Visible
Cont_Dest.set_boolean_by_name('/0/data/visible', 1)
#File Merge
#First Container
DataFields = gwyutils.get_data_fields_dir(Cont_Dest)
for key in DataFields.keys():
title = Cont_Dest.get_string_by_name(key+"/title")
if (title == 'Amplitude') : Cont_Dest.remove_by_prefix('/'+key.split('/')[1]+'/')
Cont_Dest.set_string_by_name(key+'/title', title+'.'+Files_To_Open[0])
#Rest of Containers
for filename in Files_To_Open[1:] :
#!/usr/bin/env python2
import gwy
# Set the settings for each function from the saved settings file (~/.gwyddion/settings)
s = gwy.gwy_app_settings_get()
# Turn colour bar off
s["/module/pixmap/ztype"] = 0
# Define the settings for image processing functions e.g. align rows here
# s['/module/linematch/method'] = 2
# 'align_rows' function
s["/module/linematch/direction"] = 0
s["/module/linematch/do_extract"] = False
s["/module/linematch/do_plot"] = False
s["/module/linematch/masking"] = 1
s["/module/linematch/max_degree"] = 0
s["/module/linematch/method"] = 1
s["/module/linematch/trim_fraction"] = float(0.05)
def otsuthresholdgrainfinding(data, k):
# 'align_rows' function
# s["/module/linematch/direction"] = 0
# s["/module/linematch/do_extract"] = False
# s["/module/linematch/do_plot"] = False
# s["/module/linematch/masking"] = 2
# s["/module/linematch/max_degree"] = 0
# s["/module/linematch/method"] = 0 # uses median
# s["/module/linematch/trim_fraction"] = float(0.05)
# Select channel 'k' of the file
def runbatch(root, cwd, pdr, pngexp, ratio):
# Export PNG with scalebar
s = gwy.gwy_app_settings_get()
s['/module/pixmap/title_type'] = 0
s['/module/pixmap/ztype'] = 0
s['/module/pixmap/xytype'] = 0
s['/module/pixmap/draw_maskkey'] = False
# ... (*lots* of possible settings, see ~/.gwyddion/settings)
Files_To_Open = [ f for f in listdir(cwd) if isfile(join(cwd,f)) ]
try:
mkdir(join(cwd,'Processed'))
except Exception as sym:
print ('Already Exist')
Tobe_Saved = join(cwd, 'Processed')
filename_save = cwd.split('/')[-1]
print (Files_To_Open)
#Load first file to use as Merged file
for filename in Files_To_Open:
print(filename)
try:
Temp = gwy.gwy_file_load(join(cwd,filename), RUN_NONINTERACTIVE)
print(type(Temp))
if type(Temp) == gwy.Container :
print('right type')
Cont_Dest = Temp
Files_To_Open.remove(filename)
break
Files_To_Open.remove(filename)
print('loadedbutnot')
except Exception as sym:
print('except')
print ("not proper file"+str(sym)+"\n")
continue
#Add into current browser and Make Visible on display
gwy.gwy_app_data_browser_add(Cont_Dest)
Cont_Dest.set_boolean_by_name('/0/data/visible', 1)
print (Files_To_Open)
#File Merge
#First Container
DataFields = gwyutils.get_data_fields_dir(Cont_Dest)
for key in DataFields.keys():
title = Cont_Dest.get_string_by_name(key+"/title")
if (title == 'Amplitude') : Cont_Dest.remove_by_prefix('/'+key.split('/')[1]+'/')
Cont_Dest.set_string_by_name(key+'/title', title+'.'+Files_To_Open[0])
#Rest of Containers
for filename in Files_To_Open :
#print (orgfile, join(cwd,filename))
try:
Temp_Source = gwy.gwy_file_load(join(cwd,filename), RUN_NONINTERACTIVE)
if type(Temp_Source) == gwy.Container:
Cont_Source = Temp_Source
pass
else:
continue
except Exception as sym:
print ("not proper file"+sym+"\n")
continue
DataFields = gwyutils.get_data_fields_dir(Cont_Source)
for key in DataFields.keys():
ID = key.split('/')[1]
title = Cont_Source.get_string_by_name(key+"/title")
if (title == 'Height') :
Cont_Source.set_string_by_name(key+'/title', title+'.'+filename)
gwy.gwy_app_data_browser_copy_channel(Cont_Source, int(ID), Cont_Dest)
print (key, title)
gwy_app_data_browser_remove(Cont_Source)
del Cont_Source
print (gc.collect())
#Change Palette, Flatten, Correct line, Remove Scars, Change Scale
DataFields = gwyutils.get_data_fields_dir(Cont_Dest)
for key in DataFields.keys():
ID = key.split('/')[1]
title = Cont_Dest.get_string_by_name(key+"/title")
print (title+'\n')
# Subtract polynomial background
coeffs = DataFields[key].fit_polynom(3, 3)
DataFields[key].subtract_polynom(3, 3, coeffs)
DataFields[key].data_changed()
#Get X Y scale
si = {'x' : 'um' , 'y' : 'um'}
size_x = DataFields[key].get_xreal()*1000000
if (size_x < 1.0):
size_x = size_x * 1000
si['x'] = 'nm'
size_y = DataFields[key].get_yreal()*1000000
if (size_y < 1.0):
size_y = size_y * 1000
si['y'] = 'nm'
scale = str(size_x)+si['x']+'by'+str(size_y)+si['y']
title = title + '_'+ scale
# Line and scar correction (run module functions)
gwy.gwy_app_data_browser_select_data_field(Cont_Dest, int(ID))
gwy.gwy_process_func_run("line_correct_median", Cont_Dest, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("scars_remove", Cont_Dest, gwy.RUN_IMMEDIATE)
gwy.gwy_process_func_run("fix_zero", Cont_Dest, gwy.RUN_IMMEDIATE)
#Get Color Type
colorr = Cont_Dest.get_int32_by_name('/'+ID+'/base/range-type')
#Change_Color Palette
Cont_Dest.set_string_by_name('/'+ID+'/base/palette', 'Gold')
#Get Height Distribution and get Percentile color set range
#Get CDH
histogram = gwy.DataLine(1, 1, False)
DataFields[key].cdh(histogram, 512)
data = histogram.get_data()
#Get Percentile Range
Data_Range = DataFields[key].get_min_max()
Histogram_pct = [(float(index))/512 for index, value in enumerate(data) if (data[index] >= ratio[1] and data[index-1] <= ratio[1]) or (data[index] <= ratio[0] and data[index+1] >= ratio[0])]
Range = Data_Range[1]-Data_Range[0]
Color_Range = {'min': Data_Range[0]+Range*Histogram_pct[0], 'max':Data_Range[0]+Range*Histogram_pct[1]}
Cont_Dest.set_int32_by_name('/0/base/range-type' , 1)
Cont_Dest.set_double_by_name('/0/base/min', Color_Range['min'])
Cont_Dest.set_double_by_name('/0/base/max', Color_Range['max'])
#Change Color Range into (Full:0, Manual:1, Auto:2, Adaptive:3)
Cont_Dest.set_int32_by_name('/'+ID+'/base/range-type', 2)
print (title)
gwy.gwy_file_save(Cont_Dest, Tobe_Saved+'/'+str(title)+'%d.png' % int(ID), gwy.RUN_NONINTERACTIVE)
Cont_Dest.set_boolean_by_name('/'+ID+'/data/visible', 0)
gwy.gwy_file_save(Cont_Dest,Tobe_Saved+'/'+filename_save+'.gwy', gwy.RUN_NONINTERACTIVE)
gwy_app_data_browser_remove(Cont_Dest)