def run():
c = gwy.gwy_app_data_browser_get_current(gwy.APP_CONTAINER)
filename = c['/filename']
dir_path,basename = os.path.split(filename)
basename = basename[0:-4]
#print dir_path,base_name
d = gwy.gwy_app_data_browser_get_current(gwy.APP_DATA_FIELD)
data_field_id = gwy.gwy_app_data_browser_get_current(gwy.APP_DATA_FIELD_ID)
meta_field = '/' + str(data_field_id) + '/meta'
title = '/' + str(data_field_id) + '/data/title'
channel = c[title]
#print channel
gwy.gwy_app_data_browser_select_data_field(c,data_field_id)
#meta = c[meta_field]
#print meta.keys_by_name()
#bias = meta['Bias']
#bias, bu = bias.split(' ')
#current = meta['Z controller Setpoint']
#current, cu = current.split(' ')
#current = float(current) * 1e12
#cu = 'pA'
#current_bias = 'pm'
#xd = d.get_xreal() * 1e9
#yd = d.get_yreal() * 1e9
#xyu = 'nm'
output_path = dir_path
output_name = basename + '.png'
output = os.path.join(output_path,output_name)
gwy.gwy_file_save(c, output, gwy.RUN_NONINTERACTIVE)
def savefilesasgwy(data, filename):
# Turn rulers on
s["/module/pixmap/xytype"] = 1
# Get directory path and filename (including extension to avoid overwriting .000 type Bruker files)
directory, filename = os.path.split(filename)
# Create a saving name format/directory
savedir = os.path.join(directory)
# If the folder Processed doest exist make it here
if not os.path.exists(savedir):
os.makedirs(savedir)
# Save the data for the channels found above i.e. ZSensor/Height, as chosen_ids
# Data is exported to a file of extension set in the main script
# Data is exported with the string '_processed' added to the end of its filename
gwy.gwy_app_data_browser_select_data_field(data, k)
# change the colour map for all channels (k) in the image:
palette = data.set_string_by_name("/" + str(k) + "/base/palette",
"Nanoscope.txt")
# Determine the title of each channel
# title = data["/%d/data/title" % k]
# if not title:
# title = 'unknown'
# Generate a filename to save to by removing the extension to the file, adding the suffix '_processed'
# and an extension set in the main file
savename = os.path.join(savedir, filename) + str(k) + '.gwy'
# Save the file
gwy.gwy_file_save(data, savename, gwy.RUN_NONINTERACTIVE)
def save_image_file(container, save_file):
"""Saves image file through Gwyddion, with optional file dialog.
Args:
container (gwy-container): Gwyddion container which will be exported.
save_file (str): Filepath how the file will be saved.
"""
if config.export_image_dialog:
gwy.gwy_file_save(container, save_file, gwy.RUN_INTERACTIVE)
else:
gwy.gwy_file_save(container, save_file, gwy.RUN_NONINTERACTIVE)
def save_dfield_to_png(container, datafield_name, filename, run_type):
"""
Save desired datafield given by name stored in container to file.
@param container: gwy.Container which has datafield of given name
@param datafield_name: datafield name in string representation (like '/0/data')
@param filename: expected filename
@param run_type: select of interactive (RUN_INTERACTIVE) or noninteractive mode (RUN_NONINTERACTIVE)
"""
gwy.gwy_app_data_browser_reset_visibility(container, gwy.VISIBILITY_RESET_SHOW_ALL)
datafield_num = int(datafield_name.split('/')[1])
gwy.gwy_app_data_browser_select_data_field(container, datafield_num)
gwy.gwy_file_save(container, filename, run_type)
def save_dfield_to_png(container, datafield_name, filename, run_type):
"""
Save desired datafield given by name stored in container to file.
@param container: gwy.Container which has datafield of given name
@param datafield_name: datafield name in string representation (like '/0/data')
@param filename: expected filename
@param run_type: select of interactive (RUN_INTERACTIVE) or noninteractive mode (RUN_NONINTERACTIVE)
"""
gwy.gwy_app_data_browser_reset_visibility(container,
gwy.VISIBILITY_RESET_SHOW_ALL)
datafield_num = int(datafield_name.split('/')[1])
gwy.gwy_app_data_browser_select_data_field(container, datafield_num)
gwy.gwy_file_save(container, filename, run_type)
def run(container, mode):
container = gwy.gwy_app_data_browser_get_current(gwy.APP_CONTAINER)
filename = container['/filename']
path, _ = os.path.splitext(filename)
output_path = path + OUTPUT_SUFFIX
if not os.path.exists(output_path):
os.mkdir(output_path)
for i, id_ in enumerate(gwy.gwy_app_data_browser_get_data_ids(container)):
title = container['/{}/data/title'.format(id_)]
gwy.gwy_app_data_browser_select_data_field(container, id_)
output_filename = '{:03d}_{}.{}'.format(id_, title, OUTPUT_FILESUFFIX)
output_filename = os.path.join(output_path, output_filename)
mode = gwy.RUN_INTERACTIVE if i == 0 else gwy.RUN_NONINTERACTIVE
print 'Exporting {} ...'.format(output_filename)
gwy.gwy_file_save(container, output_filename, mode)
def save_topo_bwd_data(self, path):
"""Save backward topography data file.
Args:
path (str): File path where the file should be save.
"""
self.dat_topo_bwd = os.path.join(
path,
str(self.m_id) + "_bwd." + config.dat_type_out)
gwy.gwy_file_save(self.container, self.dat_topo_bwd,
gwy.RUN_NONINTERACTIVE)
if config.dat_type_igor:
self.file_igor = os.path.join(path,
"g" + str(self.m_id) + "_ori.tb0")
shutil.move(self.dat_topo_bwd, self.file_igor)
def savecroppedfiles(directory, data, filename, extension, orig_ids, crop_ids,
minheightscale, maxheightscale):
# Save the data for the cropped channels
# Data is exported to a file of extension set in the main script
# Data is exported with the string '_cropped' added to the end of its filename
# Turn rulers off
s["/module/pixmap/xytype"] = 0
# Get directory path and filename (including extension to avoid overwriting .000 type Bruker files)
directory, filename = os.path.split(filename)
# Create a saving name format/directory
savedir = os.path.join(directory, 'Cropped')
# If the folder Cropped doest exist make it here
if not os.path.exists(savedir):
os.makedirs(savedir)
crop_directory = savedir
# Otherwise set the existing Cropped directory as the directory to write to
else:
crop_directory = savedir
# For each cropped file, save out the data with the suffix _Cropped_#
for i in range(len(orig_ids), len(crop_ids), 1):
# select each channel fo the file in turn
gwy.gwy_app_data_browser_select_data_field(data, i)
# change the colour map for all channels (k) in the image:
palette = data.set_string_by_name("/" + str(i) + "/base/palette",
"Nanoscope.txt")
# Set the image display to fixed range and the colour scale for the images
maximum_disp_value = data.set_int32_by_name(
"/" + str(i) + "/base/range-type", int(1))
minimum_disp_value = data.set_double_by_name(
"/" + str(i) + "/base/min", float(minheightscale))
maximum_disp_value = data.set_double_by_name(
"/" + str(i) + "/base/max", float(maxheightscale))
# Generate a filename to save to by removing the extension to the file and a numerical identifier (the crop no)
# The 'crop number' is the channel number minus the original number of channels, less one to avoid starting at 0
savenumber = i - (len(orig_ids) - 1)
# adding the suffix '_cropped' and adding the extension set in the main file
savename = os.path.join(
crop_directory,
filename) + '_cropped_' + str(savenumber) + str(extension)
# Save the file
gwy.gwy_file_save(data, savename, gwy.RUN_NONINTERACTIVE)
def savefiles(data, filename, extension):
# Save file scale option: 1 - ruler, 2 - inset scale bar, 0 - none
s["/module/pixmap/xytype"] = savefilesScale_option
# Get directory path and filename (including extension to avoid overwriting .000 type Bruker files)
directory, filename = os.path.split(filename)
# Create a saving name format/directory
savedir = os.path.join(directory, 'Processed')
# If the folder Processed doest exist make it here
if not os.path.exists(savedir):
os.makedirs(savedir)
# Save the data for the channels found above i.e. ZSensor/Height, as chosen_ids
# Data is exported to a file of extension set in the main script
# Data is exported with the string '_processed' added to the end of its filename
gwy.gwy_app_data_browser_select_data_field(data, k)
# change the colour map for all channels (k) in the image:
palette = data.set_string_by_name("/%s/base/palette" % k,
savefile_zscalecolour)
# Determine the title of each channel
title = data["/%d/data/title" % k]
# Generate a filename to save to by removing the extension to the file, adding the suffix '_processed'
# and an extension set in the main file
savename = os.path.join(
savedir,
filename) + str(k) + '_' + str(title) + '_processed' + str(extension)
# Save the file
gwy.gwy_file_save(data, savename, gwy.RUN_NONINTERACTIVE)
# Show the mask
data['/%d/mask' % k] = mask
# Add the sufix _masked to the previous filename
savename = os.path.join(savedir, filename) + str(k) + '_' + str(
title) + '_processed_masked' + str(extension)
# Save the data
gwy.gwy_file_save(data, savename, gwy.RUN_NONINTERACTIVE)
gwy.gwy_app_file_close()
def save_all(containers, format="svg", palette="Gray", _id=0):
"""
Saves all open files to PNG image files in a folder in image directory.
containers is a list of open containers...
...can be obtained by gwy.gwy_app_data_browser_get_containers()
"""
for c in containers:
# set palette of datafield
c.set_string_by_name("/{}/base/palette".format(_id), "Gray")
# file name
fname = gwy.gwy_file_get_filename_sys(c)
fpath, image_name = os.path.split(fname)
# save
image_name_string = "{}.{}".format(
os.path.splitext(image_name)[0], format)
save_string = os.path.join(fpath, image_name_string)
gwy.gwy_app_data_browser_select_data_field(c, _id)
gwy.gwy_file_save(c, save_string, gwy.RUN_NONINTERACTIVE)
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 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()
# from array import array
# output_file = open("%s/channel/%02d/binary" % (output_folder,i), 'wb')
# float_array = array('d', data)
# float_array.tofile(output_file)
# output_file.close()
# Save into JSON
ch_meta["data"] = data
# Save pickle
#file = open("%s/channel/%02d/image.p" % (output_folder,i), "w" )
#pickle.dump(data,file)
#file.close()
# Save binary data
#data = data_field.get_data()
# Save PNG thumbnail
gwy.gwy_file_save(container, "%s/channel/%02d/image.png" % (output_folder,i), gwy.RUN_NONINTERACTIVE)
# Save metadata
file = open("%s/channel/%02d/channel.json" % (output_folder,i), "w" )
json.dump(ch_meta,file)
file.close()
gwy.gwy_app_data_browser_remove(container)
print("%s" % (output_folder))
sys.exit()
meta = c[meta_field]
print meta.keys_by_name()
bias = meta['Bias']
bias, bu = bias.split(' ')
current = meta['Z controller Setpoint']
current, cu = current.split(' ')
current = float(current) * 1e12
cu = 'pA'
current_bias = 'pm'
xd = d.get_xreal() * 1e9
yd = d.get_yreal() * 1e9
xyu = 'nm'
print xd
print bias
temp_name = basename+'_temp.png'
gwy.gwy_file_save(c, temp_name, gwy.RUN_NONINTERACTIVE)
# prepare to save
w = d.get_xres()
h = d.get_yres()
io.use_plugin('freeimage')
data_field = '/' + str(data_field_id) + '/data'
img = Image.open(temp_name)
I = np.asarray(img)
print len(I.shape)
if len(I.shape) > 2:
new = np.zeros((w+40,h,3))
new[:,:,:] = 256
new[:w,:h,:] = I
new = new.astype('int16')
else:
# Stupid bloody /0/data/nonsense
key = "/"+str(data_set)+"/data"
data = datafields[key]
# Plane level
a, bx, by = data.fit_plane()
data.plane_level(a, bx, by)
# Median line correction
data = line_correct_median(data)
# Fix zero
data.add(-1.0 * data.get_min())
# Set colour range
base = "/"+str(data_set)+"/base"
container.set_int32_by_name(base+"/range-type", 1)
container.set_double_by_name(base+"/min", colour_min)
container.set_double_by_name(base+"/max", colour_max)
container.set_string_by_name(base+"/palette", palette)
# Do silly things required to save
gwy.gwy_app_data_browser_reset_visibility(container, gwy.VISIBILITY_RESET_SHOW_ALL)
gwy.gwy_app_data_browser_select_data_field(container, data_set)
if saved_once:
gwy.gwy_file_save(container, out_file, gwy.RUN_NONINTERACTIVE)
else:
gwy.gwy_file_save(container, out_file, gwy.RUN_INTERACTIVE)
saved_once = True
gwy.gwy_app_data_browser_reset_visibility(container, gwy.VISIBILITY_RESET_HIDE_ALL)
### SAVING THE MODIFIED FILES AS TIFFS
###
#Save all files as tiffs - this puts them all with the raw data annoyingly
#Could put in some os commands to move everything around afterwards
#Use blue and gold colour scheme with a sensible and consistent colour scale
maximum_disp_value = gwy_rawdata.set_int32_by_name(
"/" + str(i) + "/base/range-type", int(1))
minimum_disp_value = gwy_rawdata.set_double_by_name(
"/" + str(i) + "/base/min", float(1e-9))
maximum_disp_value = gwy_rawdata.set_double_by_name(
"/" + str(i) + "/base/max", float(20e-9))
palette = gwy_rawdata.set_string_by_name(
"/" + str(i) + "/base/palette", "BlueandGold")
if i == 4: #save trace and retrace seperately - presumably can do this more elegantly
saved_filename = str(image[:-4] + '_trace.tiff')
gwy.gwy_file_save(gwy_rawdata, saved_filename,
gwy.RUN_NONINTERACTIVE)
else:
saved_filename = str(image[:-4] + '_retrace.tiff')
gwy.gwy_file_save(gwy_rawdata, saved_filename,
gwy.RUN_NONINTERACTIVE)
gwy.gwy_app_data_browser_remove(
gwy_rawdata) #close the file once we've finished with it
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)
title = '/' + str(data_field_id) + '/data/title'
channel = c[title]
print channel
gwy.gwy_app_data_browser_select_data_field(c,data_field_id)
meta = c[meta_field]
print meta.keys_by_name()
bias = meta['Bias']
bias, bu = bias.split(' ')
current = meta['Z controller Setpoint']
current, cu = current.split(' ')
current = float(current) * 1e12
cu = 'pA'
current_bias = 'pm'
xd = d.get_xreal() * 1e9
yd = d.get_yreal() * 1e9
xyu = 'nm'
print xd
print bias
count = 1
output_name = basename+'_'+str(xd)+xyu+'_'+str(yd)+xyu+'_'+bias+bu+'_'+str(current)+cu+'_'+str(count)+'.png'
while os.path.exists(output_name):
count = count + 1
output_name = basename+'_'+str(xd)+xyu+'_'+str(yd)+xyu+'_'+bias+bu+'_'+str(current)+cu+'_'+str(count)+'.png'
output_path = os.path.join(dir_path,'temp')
if not os.path.isdir(output_path):
os.mkdir(output_path)
output = os.path.join(output_path,output_name)
print output
#img.save(output)
gwy.gwy_file_save(c, output, gwy.RUN_NONINTERACTIVE)
import gwy
import gwyutils
import sys
filename = sys.argv[1]
# '/Users/pabloherrero/sabat/stm_data/november19_experiments/QE1/2019-11-12-QE1_001.sxm'
f = open(filename, "r")
container = gwy.gwy_app_file_load(filename)
ids = gwy.gwy_app_data_browser_get_data_ids(container)
cons = gwy.gwy_app_data_browser_get_containers()
for c in cons:
dfields = gwyutils.get_data_fields_dir(c)
for key in dfields.keys():
datafield = dfields[key]
print(datafield.get_xreal())
gwy.gwy_app_data_browser_select_data_field(container, ids[0])
container['/%u/base/palette' % ids[0]] = 'Gold'
gwy.gwy_process_func_run("level", container, gwy.RUN_INTERACTIVE)
gwy.gwy_process_func_run("scars_remove", container, gwy.RUN_INTERACTIVE)
gwy.gwy_file_save(container, '%s-%02u.png' % (basename, 0),
gwy.RUN_NONINTERACTIVE)
