def update_image(self,widget,data):
#pass
#self.channel_id = self.combobox_channels.get_active()
gwy.gwy_app_data_browser_add(self.c)
self.load_data()
self.d.data_changed()
#print "update", self.togglebutton_level.get_active()
self.local_c.set_object_by_name(self.data_id_str+"data", self.d)
if re.search(r'Z', self.channel_str):
#print self.channel_str
self.gradient_key = 'Gwyddion.net'
elif re.search(r'Frequency', self.channel_str):
self.gradient_key = 'Gray'
self.local_c.set_string_by_name(self.data_id_str+"base/palette", self.gradient_key)
self.local_c.set_int32_by_name(self.data_id_str+"base/range-type", 1)#gwy.LAYER_BASIC_RANGE_FIXED
self.local_c.set_double_by_name(self.data_id_str+"base/min", float(self.data_min + self.scale_min_current/100*self.data_dif))
self.local_c.set_double_by_name(self.data_id_str+"base/max", float(self.data_min + self.scale_max_current/100*self.data_dif))
self.local_c[self.data_id_str+"data"].data_changed()
#print self.local_c[self.data_id_str+"base/min"],self.data_id_str+"base/min"
#print self.data_min + self.scale_min_current/100*self.data_dif,self.data_min + self.scale_max_current/100*self.data_dif
layer = gwy.LayerBasic()
layer.set_data_key(self.data_id_str+"data")
layer.set_gradient_key(self.data_id_str+"base/palette")
layer.set_range_type_key(self.data_id_str+"base")
layer.set_min_max_key(self.data_id_str+"base")
self.view.set_data_prefix(self.data_id_str+"data")
self.view.set_base_layer(layer)
#self.combobox_files.grab_focus()
gwy.gwy_app_data_browser_remove(self.c)
def update_image(self,widget,data):
#pass
for container,gwydata,view in zip(self.containers,self.gwydatas,self.views):
self.c = gwydata.get_container()
self.load_data(0,0)
gwy.gwy_app_data_browser_add(self.c)
self.d_origin = self.c[self.data_id_str + 'data']
#self.d = self.d_origin.duplicate()
if self.d_origin:
self.c.set_object_by_name(self.data_id_str + 'data',self.d_origin)
else:
self.d_origin = self.c[self.data_id_str + 'data']
gwy.gwy_app_data_browser_select_data_field(self.c,0)
#if self.togglebutton_level.get_active():
# gwy.gwy_app_data_browser_select_data_field(self.c, 0)
# gwy.gwy_process_func_run("level", self.c, gwy.RUN_IMMEDIATE)
self.d = self.c[self.data_id_str + 'data']
d_process = self.d.duplicate()
#self.data_min = self.d.get_min()
#self.data_max = self.d.get_max()
#self. data_dif = self.data_max - self.data_min
#self.scale_min_current = self.scale_min.get_value()
#self.scale_max_current = self.scale_max.get_value()
#bottom = self.data_min + self.scale_min_current/100*self.data_dif
#top = self.data_min + self.scale_max_current/100*self.data_dif
#d_process.clamp(bottom, top)
#self.d.clamp(bottom, top)
self.d = d_process
self.d.data_changed()
#print "update", self.togglebutton_level.get_active()
container.set_object_by_name(self.data_id_str+"data", self.d)
#if re.search(r'Z', self.channel_str):
#print self.channel_str
# self.gradient_key = 'Julio'
self.gradient_key = 'Julio'
#elif re.search(r'Frequency', self.channel_str):
# self.gradient_key = 'Gray'
container.set_string_by_name(self.data_id_str+"base/palette", self.gradient_key)
container.set_int32_by_name(self.data_id_str+"base/range-type", 1)#gwy.LAYER_BASIC_RANGE_FIXED
#self.local_c.set_double_by_name(self.data_id_str+"base/min", float(self.data_min + self.scale_min_current/100*self.data_dif))
#self.local_c.set_double_by_name(self.data_id_str+"base/max", float(self.data_min + self.scale_max_current/100*self.data_dif))
container[self.data_id_str+"data"].data_changed()
#print self.local_c[self.data_id_str+"base/min"],self.data_id_str+"base/min"
#print self.data_min + self.scale_min_current/100*self.data_dif,self.data_min + self.scale_max_current/100*self.data_dif
layer = gwy.LayerBasic()
layer.set_data_key(self.data_id_str+"data")
layer.set_gradient_key(self.data_id_str+"base/palette")
layer.set_range_type_key(self.data_id_str+"base")
layer.set_min_max_key(self.data_id_str+"base")
view.set_data_prefix(self.data_id_str+"data")
view.set_base_layer(layer)
#self.combobox_files.grab_focus()
gwy.gwy_app_data_browser_remove(self.c)
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 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()
### 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
