#This function does all the editing of the gwyddion settings file

#Taken out of the main text in an effort to make code more readable

#plane-subtract the data

s["/module/polylevel/col_degree"] = 3

s["/module/polylevel/do_extract"] = False

s["/module/polylevel/independent"] = True

s["/module/polylevel/masking"] = 2 #don't use any mask that might be left over

s["/module/polylevel/max_degree"] = 3

s["/module/polylevel/row_degree"] = 3

s["/module/polylevel/same_degree"] = True

#'align_rows' function

s["/module/linematch/direction"] = 0

s["/module/linematch/do_extract"] = False

s["/module/linematch/do_plot"] = False

s["/module/linematch/masking"] = 0

s["/module/linematch/max_degree"] = 1

s["/module/linematch/method"] = 1 #uses median

s["/module/linematch/trim_fraction"] = float(0.05)

#Gaussian filter to remove noise

s["/module/filter/dialog/position/height"] = 393

s["/module/filter/dialog/position/width"] = 281

s["/module/filter/filter_type"] = 7

s["/module/filter/gauss_size"] = float(1)

s["/module/filter/masking"] = 2

s["/module/filter/size"] = 5

#Shamelessly taken from Gwyddion forums - puts a height scale bar on images

s['/module/pixmap/title_type'] = 0

#s['/module/pixmap/ztype'] = 0

s['/module/pixmap/xytype'] = 2

s['/module/pixmap/draw_maskkey'] = False

s['/module/pixmap/transparent_bg'] = True

#Export image with the mask on

s['/module/pixmap/draw_mask'] = False

#Font and linewidth info

s['/module/pixmap/font'] = "Liberation Serif Bold"

s['/module/pixmap/line_width'] = float(2)

s["/module/pixmap/scale_font"] = True

s['/module/pixmap/font_size'] = float(12)

#Put a scale bar for 500 nm on the image

s['/module/pixmap/inset_draw_label'] = True

s['/module/pixmap/inset_draw_text_above'] = True

s['/module/pixmap/inset_draw_ticks'] = False

s['/module/pixmap/inset_length'] = "200 nm"

s["/module/pixmap/inset_pos"] = 3 #bottom left = 3

#Keep the original image parameters - e.g. number of pixels

s["/module/pixmap/xytype"] = 2

s["/module/pixmap/zoom"] = float(1)

datafield = container['/%d/data' % channel_ID]

# Calculate min, max and range of data to allow calculation of relative value for grain thresholding

#I think this is too 'brutal' a way of finding relative threshold

#Something like top/bottom 10% might be better

#Don't think that the otsu uses the full data range in this way

min_datarange = datafield.get_min()

max_datarange = datafield.get_max()

#print datafield.get_rms()

data_range = abs(max_datarange - min_datarange)

# Calculate Otsu threshold for data

o_threshold = datafield.otsu_threshold()

# Calculate relative threshold for grain determination

rel_threshold = (100 * (o_threshold/data_range))*sqrt(2) #Not sure this is scaling properly

# Mask grains

mask = gwy.DataField.duplicate(datafield)

datafield.grains_mark_height(mask, 30, False)

#Using grains to make a binary mask

binary_mask = mask