def load_data(filename, debug = "true"):
""" loads files into gwyydion container and returns it"""
if debug:
print("in load_data with arguments {0}".format(filename))
mode = gwy.RUN_NONINTERACTIVE
c=gwy.gwy_file_load(filename,mode)
return c
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 __init__(self, m_file, **kwargs):
self.surface = None
self.tip = None
Data.__init__(self, m_file, **kwargs)
self.set_settings()
self.container = gwy.gwy_file_load(self.m_file, gwy.RUN_NONINTERACTIVE)
gwy.gwy_app_data_browser_add(self.container)
self.img_topo_fwd = None
self.img_topo_bwd = None
self.topo_fwd_ch = self.return_topo_fwd_ch()
self.topo_bwd_ch = self.return_topo_bwd_ch()
self.size = None
self.rotation = None
self.line_time = None
self.bias = None
self.current = None
self.xoffset = None
self.yoffset = None
self.scan_duration = None
self.extract_meta(gwyddion.get_meta_ids(self.container)[0])
def convertAFM(filenamex, saveImg = True):
filename = os.path.abspath(filenamex)
# print 'Loading ', filename
for i in range(100):
c = gwy.gwy_file_load(filename, gwy.RUN_NONINTERACTIVE)
if c != None:
break
time.sleep(0.1)
if c == None:
return None, None
gwy.gwy_app_data_browser_add(c)
for key in c.keys_by_name():
if re.match(r'^/0/data$', key):
field = c[key]
xres = field.get_xres()
yres = field.get_yres()
xreal = (field.get_xreal()*1e6)/2.0
yreal = (field.get_yreal()*1e6)/2.0
weights = gwy.DataLine(xres, 1.0, True)
weights.part_fill(0, xres//3, 1.0)
filtered = gwy.DataField.new_alike(field, False)
field.fft_filter_1d(filtered, weights,
gwy.ORIENTATION_HORIZONTAL,
gwy.INTERPOLATION_ROUND)
degrees = [1,1]
field.subtract_polynom(degrees[0],degrees[1],field.fit_polynom(degrees[0],degrees[1]))
field.data_changed()
data = gwyutils.data_field_data_as_array(field)
data = np.array(data)[::,::-1]
imfilename = False
if saveImg:
filename = os.path.abspath('D:/lithography/')
imfilename = str(filename)+"/current.png"
print (imfilename)
res = saveAFMimg(data, imfilename )
writeImageMacro( imfilename , [-xreal, -yreal, xreal, yreal])
info = {'width':xreal*2, 'height':yreal*2, 'imname': imfilename}
gwy.gwy_app_data_browser_remove(c)
return data, info
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)
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:] :
print (orgfile, join(cwd,filename))
if chunk: # filter out keep-alive new chunks
f.write(chunk)
#f.flush() commented by recommendation from J.F.Sebastian
return local_filename
# Main program
## Create output folder
output_folder = "."
try:
os.makedirs("%s/" % (output_folder))
os.chdir(output_folder)
except OSError as exc:
pass
## Download file
#rawFile = download_file("http://127.0.0.1:8080%s" % path)
rawFile = path
## Gywddion load
print("Gwyddion loading %s" % rawFile)
import gwy
container = gwy.gwy_file_load(rawFile, gwy.RUN_NONINTERACTIVE)
## Save to gwy
gwy.gwy_file_save(container, "%s/data.gwy" % (output_folder),
gwy.RUN_NONINTERACTIVE)
print("%s/" % (output_folder))
sys.exit()
def load_data(self,data_path):
self.current_data = data_path
self.param['full_path'] = self.current_data
self.c = gwy.gwy_file_load(self.current_data,gwy.RUN_NONINTERACTIVE)
data_field_id = 0
data_field = '/' + str(data_field_id) + '/data'
self.d = self.c[data_field]
meta_field = '/' + str(data_field_id) + '/meta'
meta = self.c[meta_field]
# Extract bias and current, if needed
################ For Nanonis sxm file ################
if meta.contains_by_name('Bias'):
bias = meta['Bias']
self.param['bias'] = bias.split(' ')[0]
self.param['bu'] = bias.split(' ')[-1]
if meta.contains_by_name('Z controller Setpoint'):
current = meta['Z controller Setpoint']
current, cu = current.split(' ')
self.param['current'] = float(current) * 1e12
self.param['cu'] = 'pA'
################ For Createc file ##################
if meta.contains_by_name('Biasvolt[mV]'):
self.param['bias'] = meta['Biasvolt[mV]']
self.param['bu'] = 'mV'
if meta.contains_by_name('Current[A]'):
self.param['current'] = float(meta['Current[A]']) * 1e12
self.param['cu'] = 'pA'
############### For Omicron file ###################
if self.c.contains_by_name('/meta/eepa/GapVoltageControl.Voltage'):
self.param['bias'] = self.c['/meta/eepa/GapVoltageControl.Voltage']
if self.c.contains_by_name('/meta/eepa/Regulator.Setpoint_1'):
self.param['current'] = self.c['/meta/eepa/Regulator.Setpoint_1']*1e9
#current_bias = 'pm'
##### IF WANT TO SUPPORT MORE FORMATS, ADD PROCESSING CODE HERE #####
self.param['width'] = self.d.get_xreal() * 1e9
self.param['height'] = self.d.get_yreal() * 1e9
self.param['width_real'] = self.param['width'] * self.param['ratio']
self.param['height_real'] = self.param['height'] * self.param['ratio']
self.param['xyu'] = 'nm'
self.param['w_dim'] = self.d.get_xres()
self.param['h_dim'] = self.d.get_yres()
# Setting the channels
c_keys = self.c.keys_by_name()
count = 0
channels = []
for item in c_keys:
if re.search(r'title',item):
count = count + 1
print count
for i in range(0,count,2):
title = '/' + str(i) + '/data/title'
temp_title = self.c[title]
if self.param['full_path'][-3:] == 'sxm':
temp_channel, temp_directions = temp_title.split(' ')
temp_directions = temp_directions[1:-1]
elif self.param['full_path'][-6:] =='Z_mtrx':
print temp_title, temp_title.strip().split(' ')
temp_channel = temp_title.strip().split(' ')[-1]
print temp_channel
else:
temp_channel = temp_title
#print temp_directions, i
channels.append(temp_channel)
self.param['channels'] = channels
def getdata(filename):
# Open file and add data to browser
data = gwy.gwy_file_load(filename, gwy.RUN_NONINTERACTIVE)
# Add data to browser
gwy.gwy_app_data_browser_add(data)
return data
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)
gwy_rawdata['/%d/mask' % channel_ID] = binary_mask
for file_name in file_list:
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
