Hi, I didn't find a way to acces to the Telegraphed Gain of the Digi

Maybe something like <div class="highlight highlight-source-python notranslate pos

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Acces to Telegraphed Gain about pyabf HOT 4 CLOSED

Asrilioss commented on July 22, 2024

Acces to Telegraphed Gain

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Comments (4)

swharden commented on July 22, 2024 1

Maybe something like

print(myAbf._adcSection.fTelegraphAdditGain[0])

The 0 is the ADC channel, and you may need to try several numbers to get it right

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swharden commented on July 22, 2024 1

this work perfectly

Great to hear! 🚀

do you know if is a value I can change?

Interesting question! I don't think so... that is read when the ABF is first loaded, and all the data is loaded and scaled by that value when the class is initialized, so changing it later probably won't have an effect

pyABF/src/pyabf/abf.py

Lines 466 to 484 in 06247e0

    
           def _loadAndScaleData(self, fb: BufferedReader): 
        
               """Load data from the ABF file and scale it by its scaleFactor.""" 
        
               # read the data from the ABF file 
        
               fb.seek(self.dataByteStart) 
        
               raw = np.fromfile(fb, dtype=self._dtype, count=self.dataPointCount) 
        
               nRows = self.channelCount 
        
               nCols = int(self.dataPointCount/self.channelCount) 
        
               raw = np.reshape(raw, (nCols, nRows)) 
        
               raw = np.transpose(raw) 
        
               # if data is int, scale it to float32 so we can scale it 
        
               self.data = raw.astype(np.float32) 
        
               # if the data was originally an int, it must be scaled 
        
               if self._dtype == np.int16: 
        
                   for i in range(self.channelCount): 
        
                       self.data[i] = np.multiply(self.data[i], self._dataGain[i]) 
        
                       self.data[i] = np.add(self.data[i], self._dataOffset[i])

However you could probably reach in and modify what's in abf.data[channel] based on your needs, then SetSweep() calls later would returned that modified data.

Good luck!

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swharden commented on July 22, 2024

Hi @Asrilioss, this may be possible! It's a lot of info, but if you inspect the ABF header like this you may find the variable name you're looking for:

https://swharden.com/pyabf/tutorial/#inspect-the-abf-header

It will generate a report like: https://github.com/swharden/pyABF/blob/main/data/headers/2020_07_29_0062.md#adcsection

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Asrilioss commented on July 22, 2024

Yeah I just found that I need to look at header I was looking headerV2 but your faster, thanks you for your answers and a fast one, this work perfectly, do you know if is a value I can change ?
Ty

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	def _loadAndScaleData(self, fb: BufferedReader):
	"""Load data from the ABF file and scale it by its scaleFactor."""

	# read the data from the ABF file
	fb.seek(self.dataByteStart)
	raw = np.fromfile(fb, dtype=self._dtype, count=self.dataPointCount)
	nRows = self.channelCount
	nCols = int(self.dataPointCount/self.channelCount)
	raw = np.reshape(raw, (nCols, nRows))
	raw = np.transpose(raw)

	# if data is int, scale it to float32 so we can scale it
	self.data = raw.astype(np.float32)

	# if the data was originally an int, it must be scaled
	if self._dtype == np.int16:
	for i in range(self.channelCount):
	self.data[i] = np.multiply(self.data[i], self._dataGain[i])
	self.data[i] = np.add(self.data[i], self._dataOffset[i])