"li" variable not defined in ITM.py

[jablevin]

When running >>> res = AI.get_raw_spectrum(ROI=[ROI1, ROI2], prog=True, sf=sf, k0=k0) I get the error that local variable "li" is referenced before assignment.

The code from the file is below. The error arises near the end "for k in li"

elif type(ROI) in [list, tuple]:
            multi_roi = True
           Spectrum = np.zeros((number_channels, len(ROI)), dtype=np.float32)
            for s in T:
                raw = self.get_raw_raw_data(s)
                rawv = struct.unpack('<{}I'.format(len(raw)//4), raw)
                i = 0
                while i < len(rawv):
                    b = rawv[i]
                    if b & 0xc000000000:
                        x = b & 0x0fffffff
                        y = rawv[i+1] & 0x0fffffff
                        dt = dts[x]
                        fp = dt%1
                        ip = int(dt)
                        li = []
                        for k, R in enumerate(ROI):
                            if R[y,x]:
                                li.append(k)
                        i += 3
                    else:
                        for k in li:
                                Spectrum[b-ip, k] += (1-fp)
                                Spectrum[b-ip-1, k] += fp
                        i += 1

[scholi]

There is definitely a python bug, but I'm not sure to remember correctly how the rawSpectrum is encoded to correct it and beeing sure that the data you get make sense.... I guess you should predefine li before the while. So add

li=[]

at line 1050

Can you test it with your data and tell me if the results make sens?

[scholi]

Can I get some feedback? Does this solution works?

[andrealucero]

Hello. I have a similar error when I try to run the following cell from the "Introduction to pySPM a python library for ToF-SIMS data analysis": AI = pySPM.ITM(get_data("Cysteine_B3p_p_01.itm")) sf, k0 = A.auto_mass_cal() try:

Reconstruction is a slow porcess, so the data are stored in order to speed up the running speed of this notebook

res = pySPM.utils.load("Intro_pySPM_tofsims", 'Cysteine_ROI')

except: res = AI.get_raw_spectrum(ROI=[ROI1, ROI2], prog=True, sf=sf, k0=k0) pySPM.utils.save("Intro_pySPM_tofsims", Cysteine_ROI=res)

The error is:

---

OSError Traceback (most recent call last)

in 4 # Reconstruction is a slow porcess, so the data are stored in order to speed up the running speed of this notebook ----> 5 res = pySPM.utils.load("Intro_pySPM_tofsims", 'Cysteine_ROI') 6 except: ~\Anaconda3\lib\site-packages\pySPM\utils\save.py in load(filename, *keys) 92 """ ---> 93 filename = findPKZ(filename) 94 if len(keys) == 0: ~\Anaconda3\lib\site-packages\pySPM\utils\save.py in findPKZ(filename) 36 if not os.path.exists(filename): ---> 37 raise IOError("File \"{}\" not found".format(filename)) 38 return filename OSError: File "Intro_pySPM_tofsims.pkz" not found During handling of the above exception, another exception occurred: UnboundLocalError Traceback (most recent call last) in 5 res = pySPM.utils.load("Intro_pySPM_tofsims", 'Cysteine_ROI') 6 except: ----> 7 res = AI.get_raw_spectrum(ROI=[ROI1, ROI2], prog=True, sf=sf, k0=k0) 8 pySPM.utils.save("Intro_pySPM_tofsims", Cysteine_ROI=res) ~\Anaconda3\lib\site-packages\pySPM\ITM.py in get_raw_spectrum(self, scans, ROI, FOVcorr, deadTimeCorr, **kargs) 1063 li.append(k) 1064 i += 3 -> 1065 else: 1066 for k in li: 1067 Spectrum[b-ip, k] += (1-fp) UnboundLocalError: local variable 'li' referenced before assignment Looks like it's not only the assignment of "li". I'm not an expert, so I would appreciate your help. Thank you in advance. Update 23/08/21 Tried again and the code in the cell worked

[scholi]

and? did you try the proposed solution? Does it work?

[andrealucero]

Yes. I did what you suggested before and it worked. Thank you!

[scholi]

OK. I'll add it for next release then. Thank you for the feedback.