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Adding FIXME's

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This commit is contained in:
halvorhv 2022-06-15 13:21:26 +02:00
parent 8ce1557439
commit 7676bd06af
1 changed files with 8 additions and 18 deletions
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26
nafuma/xanes/calib.py
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@ -7,18 +7,12 @@ import nafuma.xanes as xas
import nafuma.xanes.io as io import nafuma.xanes.io as io
from scipy.signal import savgol_filter from scipy.signal import savgol_filter
def rbkerbest():
print("ROSENBORG!<3")
#def split_xanes_scan(filename, destination=None):
# with open(filename, 'r') as f:
##Better to make a new function that loops through the files, and performing the split_xanes_scan on ##Better to make a new function that loops through the files, and performing the split_xanes_scan on
#Tryiung to make a function that can decide which edge it is based on the first ZapEnergy-value #Trying to make a function that can decide which edge it is based on the first ZapEnergy-value
def finding_edge(df): def finding_edge(df):
#FIXME add Fe and Co
if 5.9 < df["ZapEnergy"][0] < 6.5: if 5.9 < df["ZapEnergy"][0] < 6.5:
edge='Mn' edge='Mn'
return(edge) return(edge)
@ -26,12 +20,8 @@ def finding_edge(df):
edge='Ni' edge='Ni'
return(edge) return(edge)
#def pre_edge_subtraction(df,filenames, options={}):
def test(innmat):
df_test= xas.io.put_in_dataframe(innmat)
#print(df_test)
def pre_edge_subtraction(path, options={}): def pre_edge_subtraction(path, options={}):
#FIXME add log-file instead of the troubleshoot-option
required_options = ['print','troubleshoot'] required_options = ['print','troubleshoot']
default_options = { default_options = {
'print': False, 'print': False,
@ -46,7 +36,7 @@ def pre_edge_subtraction(path, options={}):
#Defining the end of the region used to define the background, thus start of the edge #Defining the end of the region used to define the background, thus start of the edge
#######================================================================================================================================================ #######================================================================================================================================================
#Trying to implement automatical region determination based on an estimate of the edge shift #FIXME Trying to implement automatical region determination based on an estimate of the edge shift
#print(df) #print(df)
#estimated_edge_shift, df_diff, df_diff_max = find_pos_maxdiff(df, filenames,options=options) #estimated_edge_shift, df_diff, df_diff_max = find_pos_maxdiff(df, filenames,options=options)
@ -122,8 +112,8 @@ def pre_edge_subtraction(path, options={}):
return df_bkgd_sub,filenames,edge return df_bkgd_sub,filenames,edge
def post_edge_normalization(path, options={}): def post_edge_fit(path, options={}):
#FIXME should be called "fitting post edge" (normalization is not done here, need edge shift position)
required_options = ['print'] required_options = ['print']
default_options = { default_options = {
'print': False 'print': False
@ -132,7 +122,7 @@ def post_edge_normalization(path, options={}):
df_bkgd_sub,filenames,edge = pre_edge_subtraction(path, options=options) df_bkgd_sub,filenames,edge = pre_edge_subtraction(path, options=options)
#Defining the end of the pre-edge-region for Mn/Ni, thus start of the edge #Defining the end of the pre-edge-region for Mn/Ni, thus start of the edge
#Implement widget #FIXME Use rought edge shift estimate, add X eV as first guess, have an option to adjust this value with widget
if edge == 'Mn': if edge == 'Mn':
edge_stop = 6.565 edge_stop = 6.565
if edge == 'Ni': if edge == 'Ni':
@ -171,7 +161,7 @@ def smoothing(path, options={}):
} }
options = aux.update_options(options=options, required_options=required_options, default_options=default_options) options = aux.update_options(options=options, required_options=required_options, default_options=default_options)
df_bkgd_sub, df_postedge, filenames, edge = post_edge_normalization(path,options=options) df_bkgd_sub, df_postedge, filenames, edge = post_edge_fit(path,options=options)
#================= SMOOTHING #================= SMOOTHING
df_smooth = pd.DataFrame(df_bkgd_sub["ZapEnergy"]) df_smooth = pd.DataFrame(df_bkgd_sub["ZapEnergy"])
df_default = pd.DataFrame(df_bkgd_sub["ZapEnergy"]) df_default = pd.DataFrame(df_bkgd_sub["ZapEnergy"])