add calibration #2
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| a, b = symbols('a b') | ||
| eq1 = Eq((((t1 * time_res - b)/a) ** 2 - m1) , 0) | ||
| eq2 = Eq((((t2 * time_res - b)/a) ** 2 - m2) , 0) | ||
| sol = solve((eq1 , eq2) , (a , b)) |
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is there not a reliable closed form solution for this? The expression
only has 4 solutions, and I think the "correct" one would be fairly consistent if similar calibration parameters are applied from usage to usage.
Open to opinions on that of course
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yes I agree. tbh I related on leeat's previous code and didn't solve it myself. would you be ok with selecting the solution that is the closes to the current calibration? something like that:
def calibrate_spectrum(t1 , m1 , t2 , m2 , mass_gain , mass_offset, time_res: float=500e-6):
sign1 = np.array([1 , 1 , -1 , -1])
sign2 = np.array([1 , -1 , 1 , -1])
a = (t1 - t2) * t_res / (sign1 * np.sqrt(m1) + sign2 * np.sqrt(m2))
b = (sign1 * np.sqrt(m2) * t1 + sign2 * np.sqrt(m1) * t2) * t_res / (sign1 * np.sqrt(m2) + sign2 * np.sqrt(m1))
idx = np.argmin((a - mass_gain) ** 2 + (b - mass_offset) ** 2)
return a[idx] , b[idx]
| def get_spectra_df(TimeOffset): | ||
| data = collections.Counter(TimeOffset) |
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TimeOffset -> time_offset, just for syntax consistency. Also, I'm adding some docstrings to some of the other functions. Those might already be merged in (can't remember at the moment tbh), but either way, some docstrings here would be handy. For example:
def get_spectra_df(time_offset):
"""Creates formatted pandas dataframe from spectra data
Args:
time_offset (type_of_time_offset (e.g dict, list, etc)):
time offsets
Returns:
pd.DataFrame:
count spectra
"""
# rest of function
| def extract_bin_files(data_dir: str, out_dir: str, | ||
| include_fovs: Union[List[str], None] = None, | ||
| panel: Union[Tuple[float, float], pd.DataFrame] = (-0.3, 0.0), | ||
| intensities: Union[bool, List[str]] = False, time_res: float=500e-6, | ||
| timeout=100): | ||
| timeout=100 , calibration: Union[Tuple[float, float], str] = 'auto'): |
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nice! thanks for adding the type signature and giving it a default arg!
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@azulaynofar @ngreenwald any plans on continuing development of this PR? |
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