def test_datzygo_reader(wfile=None):
import os
import matplotlib.pyplot as plt
from pySurf.data2D import plot_data
from pySurf.data2D_class import Data2D
from pySurf.readers.format_reader import datzygo_reader
if wfile is None:
#relpath
wfile = r'/Volumes/GoogleDrive/Il mio Drive/progetti/sandwich/dati/09_02_27/botta di culo 1a.dat'
#wfile= os.path.join(os.path.dirname(__file__),relpath)
(d1, x1, y1) = datzygo_reader(wfile)
dd1 = Data2D(d1, x1, y1)
dd2 = Data2D(f, reader=datzygo_reader)
plt.figure()
plt.suptitle(wfile)
plt.subplot(121)
plt.title('object from data')
dd1.plot(aspect='equal')
plt.subplot(122)
plt.title('object from reader ')
dd2.plot(aspect='equal')
return dd2
def plot_repeat(rfiles,outfile=None,dis=True,name = "",plot_func=plot_data_repeat_leveling,ro=None):
"""Functions to plot a list of files side to side (e.g. repeatability or reproducibility)
with different levelings. Return list of Data2D objects.
plot_func is a function that accepts a dlist and possibly accepts arguments
outfile, dis and name (it can have them ignored in **kwargs, or not passed at all to plot_repeat).
This way, becomes a wrapper around plot_func (that doesn't necessarily have to plot,
just have an interface outfile, dis, name.
2019/04/08 made function general.
2018/11/02 moved to scripts. Modified to make it format independent acting on
data rather than on file extracting the data part in outer routine plot_data_repeat_leveling
in ."""
plt.close('all')
if ro is None:
ro={'reader':fitsWFS_reader,
'scale':(-1,-1,1),
'units':['mm','mm','um'],
'ytox':220/200,
'ypix':101.6/120,
'center':(0,0)}
#if name is None:
# name = os.path.basename(outfile) if outfile is not None else ""
dlist=[Data2D(file=wf1,**ro).level() for i,wf1 in enumerate(rfiles)]
res = plot_func(dlist,outfile=outfile,dis=dis,name = name)
return dlist
def process_set2(flist,names,outname,crop=None,dis=True):
# from C1S15_4D_DI_calibration_181031.ipynb
# called with:
ypix=None #0.127901442999 #mm
ytox=220./200.
zscale=None #0.6328
scale=(1000,-1000,0.001)
outfolder=os.path.dirname(outname)
outname=os.path.basename(outname)
dlist=[Data2D(*matrix4D_reader(wf2,scale=scale,zscale=zscale,
ypix=ypix,ytox=ytox,center=(0,0),strip=True),name=n,units=['mm','mm','um'])
for wf2,n in zip(flist,names)]
np.mean(dlist).save(os.path.join(outfolder,outname+'_avg.dat'))
plt.close('all')
sx,sy=find_grid_size(len(dlist),3)
f,axes=plt.subplots(sx,sy,sharex=True,sharey=True)
for ax,d in zip(axes.flatten(),dlist):
plt.sca(ax)
d.plot()
plt.clim(*remove_outliers(d.data,nsigma=2,itmax=3,span=1))
for ax in axes.flatten()[:len(dlist)-1:-1]:
f.delaxes(ax)
maximize()
plt.pause(0.1)
plt.tight_layout(rect=[0,0,1,0.9])
plt.suptitle ('Surfaces')
if dis:
display(plt.gcf())
plt.savefig(os.path.join(outfolder,outname+'.png'))
m_repr=[dcouples_plot([dd for dd in dlist])]
if dis:
display(plt.gcf())
plt.savefig(os.path.join(outfolder,'diff_'+outname+'.png'))
if crop is not None:
dc=[d.crop(*crop).level() for d in dlist]
m_repr=[dcouples_plot([dd for dd in dc])]
if dis:
display(plt.gcf())
plt.savefig(os.path.join(outfolder,'diff_'+outname+'_crop.png'))
return dlist
"""INPUT SETTINGS"""
plt.ion()
infolder = "G:\\My Drive\\materialsLabShared\\WFS_BONDING_TESTS\\181016_PCO2S06_Reproducibility"
file1 = "181016_01_PCO2S06_1009_08.fits"
file2 = "181016_02_PCO2S06_1009_08.fits"
scale = 101.6 / 116 #ratio between mm and pixels
ytox = 220. / 200 #aspect ratio of pixel
strip = True # strip nan frame
""""""
rfiles = [os.path.join(infolder, f) for f in [file1, file1]]
dlist = [
Data2D(*fitsWFS_reader(f,
scale=(scale, scale, 1),
center=(0, 0),
strip=strip,
ytox=ytox,
ypix=1),
units=['mm', 'mm', 'um']) for f in rfiles
]
#dlist[1]=dlist[1].rotate(1.5) #rotate 1.5 deg for test
dl = [d.level((10, 0)) for d in dlist]
mref, mtrans = align_interactive(
dl) #with default argument return transformation to first coordinates
#work on individual data files (can be replaced by functions in WFS_repeatability to work on N files:
d1, d2 = dlist
d2t = d1.apply_transform(mtrans[1])
plt.figure()
diff = plot_difference(d1, d2t)
# Similarly, routines operating on profiles (y as a function of x as couples of vector x and y), are contained in class `pyProfile.Profile` and `pyProfile.profile` which have in many points interfaces similar to modules in `pySurf`. # # Here we will focus on `Data2D` object interface. # # A first way to initialize such an object is by passing directly 2D data, (optionally) coordinates and options. # # # %% nx = 200 ny = 300 data = np.random.random(nx*ny).reshape(ny,nx) x = np.arange(nx)*25 y = np.arange(ny)*10 D = Data2D(data,x,y,units=['mm','mm','um']) #D.plot() # %% D.plot() # %% infolder=r'..\..\test\input_data\4D\180215_C1S06_cut' fn = '180215_C1S01_RefSub.csv' file = os.path.join(infolder,fn) # %% from pySurf.data2D_class import Data2D from pySurf.instrumentReader import matrix4D_reader
r = find_internal_rectangle(a, x, y)
plot_poly([[r[0][0], r[1][0]], [r[0][1], r[1][0]], [r[0][1], r[1][1]],
[r[0][0], r[1][1]], [r[0][0], r[1][0]]])
# plt.figure()
if __name__ == "__main__":
# %%TEST
nx, ny = 700, 500
a = np.zeros(nx * ny).reshape(ny, nx)
x = np.arange(nx) * 3 - 300
y = np.arange(ny) * 5 - 500
gd = Data2D(a, x, y, name='test_data')
#gd.data[40:60,150:160]=1
#gd.data[400:420,300:310]=1
#gd.data[80:100,420:440]=1
gd.data[50:60, 40:60] = 1
gd.data[300:310, 600:620] = 1
gd.data[420:440, 80:100] = 1
gd.data[50:60, 340:360] = 1
gd.data[420:440, 330:350] = 1
gd.data[250:260, 40:60] = 1
plt.close('all')
"""Despite differemt conventions, from
https://docs.python.org/3/distutils/sourcedist.html
test/test*.py is included in manifest."""
# import pyxsurf
# pyxsurf.pySurf #fails
print("TRY: import pySurf")
import pySurf
print("OK\n")
# >>> pySurf.data2D_class #fails
print("import Data2D pyxsurf.pySurf.data2D_class ")
from pySurf.data2D_class import Data2D
print("OK\nData2D is:")
print(Data2D)
print("\n")
## <module 'pyxsurf.pySurf.hello' from 'C:\\Users\\User\\AppData\\Local\\Packages\\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\\LocalCache\\local-packages\\Python37\\site-packages\\pyxsurf\\pySurf\\hello.py'>
# hello.hello() #fails
print("Initialize empty Data2D object in `a`:")
a = Data2D()
print("---")
print(a)
print("Import points from pySurf as a module:")
from pySurf import points
print(points)
def display_diff(f1,f2,data=False,dis=True,crd=None):
"""calculates, plots and returns the difference of two data.
It is just a diff-and-plot with a few added options and settings for color scale and reading files,
can probably be replaced by more standard routines.
f1 and f2 are file names, unless data is set, in that case they are interpreted as data.
Data are plotted on common color scale, while range for difference crd can be imposed,
otherwise is calculated on outlier removed difference."""
#set units
units=['mm','mm','nm']
zscale=1000
#load data in d1 and d2 according if arguments are data or filenames
if not(data):
d1=Data2D(file=f1,units=units,scale=(1000,-1000,zscale),center=(0,0))
if f2 is not None:
d2=Data2D(file=f2,units=units,scale=(1000,-1000,zscale),center=(0,0))
else:
d2=cp.deepcopy(d1)*0
#d2.data=d2.data*0
else:
d1=Data2D(f1.data,f1.x,f1.y,units=units)
if f2 is not None:
d2=Data2D(f2.data,f2.x,f2.y,units=units)
else:
d2=cp.deepcopy(d1)*0
#d2.data=d2.data*0
#plane level and diff
d1=d1.level()
d2=d2.level()
diff=(d1-d2).level()
#calculate common color range
cr1=remove_outliers(d1.data,span=True)
cr2=remove_outliers(d2.data,span=True)
cr=[min([cr1[0],cr2[0]]),max([cr1[0],cr2[1]])]
if crd is None: #color range for difference.
crd=remove_outliers(diff.data,span=True)
#plot on three panels, prints stats
plt.clf()
plt.subplot(311)
maximize()
d1.plot()
plt.clim(*cr)
d1.printstats()
plt.subplot(312)
d2.plot()
plt.clim(*cr)
d2.printstats()
plt.subplot(313)
diff.plot()
plt.clim(*crd)
print ("diff 2 - 1 = ")
diff.printstats()
plt.tight_layout()
#plt.clim(*cr)#[-0.0001,0.0001])
if not(data):
if f2 is not None:
plt.title ('Difference %s - %s'%tuple(os.path.basename(ff) for ff in [f1,f2]))
else:
plt.title ('%s '%f2)
plt.show()
#print ("PV: ",span(diff.data,size=True),diff.units[-1])
#print ("rms: ",np.nanstd(diff.data),diff.units[-1])
return d1,d2,diff
except NoOptionError:
logging.info('option ' + cgtag + ' not found')
#print('option '+cgtag+' not found')
pass
return imgdic
if __name__ == "__main__":
import os
from pySurf.data2D_class import Data2D
datafolder = r'G:\My Drive\progetti\c_overcoating\esperimenti\20210129_dopamine\20210224_dopamine_clean'
fn = 'Image00053.nid'
file_name = os.path.join(datafolder, fn)
#file_name=r'C:\Users\kovor\Documents\python\pyXTel\pySurf\test\input_data\AFM\02_test.nid'
datadic = read_nid(file_name)
data, x, y = datadic['Gr0-Ch1']
print("read data of shape", data.shape)
d = Data2D(data,
x,
y,
units=['mm', 'mm', 'um'],
scale=[1000., 1000., 1000000.])
d.plot()
plt.show()