debug and nwe functions

Analyser/FitAnalyser.py

@@ -1,4 +1,5 @@
 import numpy as np
+from uncertainties import ufloat
 
 import lmfit
 from lmfit.models import (ConstantModel, ComplexConstantModel, LinearModel, QuadraticModel,
@@ -200,16 +201,22 @@ class TwoGaussian2dModel(Model):
         self.helperModel = Gaussian2dModel()
         
         super().__init__(two_gaussian2d, **kwargs)
+        
+        self._set_paramhints_prefix()
+
+    def _set_paramhints_prefix(self):
+        self.set_param_hint('delta', value=-1, max=0)
+        self.set_param_hint('A_sigmax', expr=f'{self.prefix}delta + {self.prefix}B_sigmax')
 
     def guess(self, data, x, y, negative=False, **kwargs):
         pars_guess = guess_from_peak2d(self.helperModel, data, x, y, negative)
-        pars = self.make_params(A_amplitude=pars_guess['amplitude'], A_centerx=pars_guess['centerx'], A_centery=pars_guess['centery'],
-                             A_sigmax=pars_guess['sigmax'], A_sigmay=pars_guess['sigmay'], 
-                             B_amplitude=pars_guess['amplitude'], B_centerx=pars_guess['centerx'], B_centery=pars_guess['centery'],
-                             B_sigmax=pars_guess['sigmax'], B_sigmay=pars_guess['sigmay'])
+        pars = self.make_params(A_amplitude=pars_guess['amplitude'].value, A_centerx=pars_guess['centerx'].value, A_centery=pars_guess['centery'].value,
+                             A_sigmax=pars_guess['sigmax'].value, A_sigmay=pars_guess['sigmay'].value, 
+                             B_amplitude=pars_guess['amplitude'].value, B_centerx=pars_guess['centerx'].value, B_centery=pars_guess['centery'].value,
+                             B_sigmax=pars_guess['sigmax'].value, B_sigmay=pars_guess['sigmay'].value)
         
-        pars.add(f'{self.prefix}delta', value=-1, max=0, vary=True)
         pars[f'{self.prefix}A_sigmax'].set(expr=f'delta + {self.prefix}B_sigmax')
+        pars.add(f'{self.prefix}delta', value=-1, max=0, min=-np.inf, vary=True)
         pars[f'{self.prefix}A_sigmay'].set(min=0.0)
         pars[f'{self.prefix}B_sigmax'].set(min=0.0)
         pars[f'{self.prefix}B_sigmay'].set(min=0.0)
@@ -263,6 +270,29 @@ class FitAnalyser():
             self.fitModel = fitModel
         
         self.fitDim = fitDim
+
+    def print_params_set_templet(self, params=None):
+        
+        if params is None:
+            params = self.fitModel.make_params()
+        
+        for key in params:
+            res = "params.add("
+            res += "name=\"" + key + "\", "
+            if not params[key].expr is None:
+                res += "expr=" + params[key].expr +")"
+            else:
+                res += "value=" + f'{params[key].value:3g}' + ", "
+                if str(params[key].max)=="inf":
+                    res += "max=np.inf, "
+                else:
+                    res += "max=" + f'{params[key].max:3g}' + ", "
+                if str(params[key].min)=="-inf":
+                    res += "min=-np.inf, "
+                else:
+                    res += "min=" + f'{params[key].min:3g}' + ", "
+                res += "vary=" + str(params[key].vary) + ")"
+            print(res)
     
     def _guess_1D(self, data, x, **kwargs):
         return self.fitModel.guess(data=data, x=x, **kwargs)
@@ -373,29 +403,29 @@ class FitAnalyser():
                 'keep_attrs': keep_attrs,
             }
         )
-
-        if input_core_dims is None:
-            kwargs.update(
-                {
-                    "input_core_dims": [['x'], []],
-                }
-            )
-
-        if x is None:
-            if 'x' in dataArray.dims:
-                x = dataArray['x'].to_numpy()
-        else:
-            if isinstance(x, str):
-                if input_core_dims is None:
-                    kwargs.update(
-                        {
-                            "input_core_dims": [[x], []],
-                        }
-                    )
-                x = dataArray[x].to_numpy()
         
         if isinstance(paramsArray, type(self.fitModel.make_params())):
 
+            if input_core_dims is None:
+                kwargs.update(
+                    {
+                        "input_core_dims": [['x']],
+                    }
+                )
+
+            if x is None:
+                if 'x' in dataArray.dims:
+                    x = dataArray['x'].to_numpy()
+            else:
+                if isinstance(x, str):
+                    if input_core_dims is None:
+                        kwargs.update(
+                            {
+                                "input_core_dims": [[x]],
+                            }
+                        )
+                    x = dataArray[x].to_numpy()
+
             if self.fitDim == 1:
                 return xr.apply_ufunc(self._fit_1D, dataArray, kwargs={'params':paramsArray,'x':x},
                                         output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], 
@@ -409,7 +439,7 @@ class FitAnalyser():
                     if input_core_dims is None:
                         kwargs.update(
                             {
-                                "input_core_dims": [['x', 'y'], []],
+                                "input_core_dims": [['x', 'y']],
                             }
                         )
                 else:
@@ -419,7 +449,7 @@ class FitAnalyser():
                     elif input_core_dims is None:
                         kwargs.update(
                             {
-                                "input_core_dims": [['x', 'y'], []],
+                                "input_core_dims": [['x', 'y']],
                             }
                         )
                 
@@ -436,6 +466,27 @@ class FitAnalyser():
                                         **kwargs)
 
         else:
+
+            if input_core_dims is None:
+                kwargs.update(
+                    {
+                        "input_core_dims": [['x'], []],
+                    }
+                )
+
+            if x is None:
+                if 'x' in dataArray.dims:
+                    x = dataArray['x'].to_numpy()
+            else:
+                if isinstance(x, str):
+                    if input_core_dims is None:
+                        kwargs.update(
+                            {
+                                "input_core_dims": [[x], []],
+                            }
+                        )
+                    x = dataArray[x].to_numpy()
+
             if self.fitDim == 1:
                 return xr.apply_ufunc(self._fit_1D, dataArray, paramsArray, kwargs={'x':x},
                                         output_dtypes=[type(lmfit.model.ModelResult(self.fitModel, self.fitModel.make_params()))], 
@@ -537,4 +588,131 @@ class FitAnalyser():
 
             return xr.apply_ufunc(self._eval_2D, fitResultArray, kwargs={"x":_x, "y":_y, "shape":(len(x), len(y))}, **kwargs)
 
-            
+    def _get_fit_value_single(self, fitResult, key):
+        return fitResult.params[key].value
+
+    def _get_fit_value(self, fitResult, params):
+        func = np.vectorize(self._get_fit_value_single)
+        res = tuple(
+                func(fitResult, key)
+                for key in params
+            )
+
+        return res
+
+    def get_fit_value(self, fitResult, dask='parallelized', **kwargs):
+        firstIndex = {
+            key: fitResult[key][0]
+            for key in fitResult.dims
+            }
+        firstFitResult = fitResult.sel(firstIndex).item()
+
+        params = list(firstFitResult.params.keys())
+
+        output_core_dims=[ [] for _ in range(len(params))]
+
+        kwargs.update(
+            {
+                "dask": dask,
+                "output_core_dims": output_core_dims,
+            }
+        )
+
+        value = xr.apply_ufunc(self._get_fit_value, fitResult, kwargs=dict(params=params), **kwargs)
+
+        value = xr.Dataset(
+            data_vars={
+                params[i]: value[i]
+                for i in range(len(params))
+            },
+            attrs=fitResult.attrs
+        )
+
+        return value
+
+    def _get_fit_std_single(self, fitResult, key):
+        return fitResult.params[key].stderr
+
+    def _get_fit_std(self, fitResult, params):
+        func = np.vectorize(self._get_fit_std_single)
+        res = tuple(
+                func(fitResult, key)
+                for key in params
+            )
+
+        return res
+
+    def get_fit_std(self, fitResult, dask='parallelized', **kwargs):
+        firstIndex = {
+            key: fitResult[key][0]
+            for key in fitResult.dims
+            }
+        firstFitResult = fitResult.sel(firstIndex).item()
+
+        params = list(firstFitResult.params.keys())
+
+        output_core_dims=[ [] for _ in range(len(params))]
+
+        kwargs.update(
+            {
+                "dask": dask,
+                "output_core_dims": output_core_dims,
+            }
+        )
+
+        value = xr.apply_ufunc(self._get_fit_std, fitResult, kwargs=dict(params=params), **kwargs)
+
+        value = xr.Dataset(
+            data_vars={
+                params[i]: value[i]
+                for i in range(len(params))
+            },
+            attrs=fitResult.attrs
+        )
+
+        return value
+
+    def _get_fit_full_result_single(self, fitResult, key):
+        return ufloat(fitResult.params[key].value, fitResult.params[key].stderr)
+
+    def _get_fit_full_result(self, fitResult, params):
+        func = np.vectorize(self._get_fit_full_result_single)
+        res = tuple(
+                func(fitResult, key)
+                for key in params
+            )
+
+        return res
+
+    def get_fit_full_result(self, fitResult, dask='parallelized', **kwargs):
+        firstIndex = {
+            key: fitResult[key][0]
+            for key in fitResult.dims
+            }
+        firstFitResult = fitResult.sel(firstIndex).item()
+
+        params = list(firstFitResult.params.keys())
+
+        output_core_dims=[ [] for _ in range(len(params))]
+
+        kwargs.update(
+            {
+                "dask": dask,
+                "output_core_dims": output_core_dims,
+            }
+        )
+
+        value = xr.apply_ufunc(self._get_fit_full_result, fitResult, kwargs=dict(params=params), **kwargs)
+
+        value = xr.Dataset(
+            data_vars={
+                params[i]: value[i]
+                for i in range(len(params))
+            },
+            attrs=fitResult.attrs
+        )
+
+        return value
+    
+
+                

DataContainer/ReadData.py

@@ -3,6 +3,8 @@ import numpy as np
 from collections import OrderedDict
 from functools import partial
 import copy
+import glob
+import os
 
 
 def _read_globals_attrs(variable_attrs, context=None):
@@ -74,6 +76,9 @@ def _read_globals_attrs(variable_attrs, context=None):
         }
     )
 
+    # if result['scanAxis'] == []:
+    #     result['scanAxis'] = ['runs',]
+
     return result
 
 
@@ -83,16 +88,18 @@ def _read_shot_number_from_hdf5(x):
     return x.assign(shotNum=shotNum)
 
 
-def _assign_scan_axis_partial(x, datesetOfGlobal):
+def _assign_scan_axis_partial(x, datesetOfGlobal, fullFilePath):
     scanAxis = datesetOfGlobal.scanAxis
-    filePath = x.encoding["source"]
-    shotNum = filePath.split("_")[-1].split("_")[-1].split(".")[0]
+    filePath = x.encoding["source"].replace("\\", "/")
+    shotNum = np.where(fullFilePath==filePath)
+    shotNum = np.squeeze(shotNum)
+    # shotNum = filePath.split("_")[-1].split("_")[-1].split(".")[0]
     x = x.assign(shotNum=shotNum)
     x = x.expand_dims(list(scanAxis))
-    
+
     return x.assign_coords(
         {
-            key: np.atleast_1d(datesetOfGlobal.attrs[key][int(shotNum)])
+            key: np.atleast_1d(np.atleast_1d(datesetOfGlobal.attrs[key])[int(shotNum)])
             for key in scanAxis
         }
     )
@@ -108,6 +115,21 @@ def update_hdf5_file():
 
 def read_hdf5_file(filePath, group=None, datesetOfGlobal=None, preprocess=None, join="outer", parallel=True, engine="h5netcdf", phony_dims="access", **kwargs):
 
+    filePath = np.sort(np.atleast_1d(filePath))
+
+    filePathAbs = []
+
+    for i in range(len(filePath)):
+        filePathAbs.append(os.path.abspath(filePath[i]).replace("\\", "/"))
+
+    fullFilePath = []
+    for i in range(len(filePathAbs)):
+        fullFilePath.append(list(np.sort(glob.glob(filePathAbs[i]))))
+    fullFilePath = np.array(fullFilePath).flatten()
+
+    for i in range(len(fullFilePath)):
+        fullFilePath[i] = fullFilePath[i].replace("\\", "/")
+
     kwargs.update(
         {
             'join': join, 
@@ -120,7 +142,7 @@ def read_hdf5_file(filePath, group=None, datesetOfGlobal=None, preprocess=None,
 
     if datesetOfGlobal is None:
         datesetOfGlobal = xr.open_mfdataset(
-            filePath, 
+            fullFilePath, 
             group="globals", 
             concat_dim="fileNum", 
             combine="nested", 
@@ -130,14 +152,14 @@ def read_hdf5_file(filePath, group=None, datesetOfGlobal=None, preprocess=None,
             combine_attrs=_read_globals_attrs,
             parallel=True, )
     
-    _assgin_scan_axis = partial(_assign_scan_axis_partial, datesetOfGlobal=datesetOfGlobal)
+    _assgin_scan_axis = partial(_assign_scan_axis_partial, datesetOfGlobal=datesetOfGlobal, fullFilePath=fullFilePath)
 
     if preprocess is None:
         kwargs.update({'preprocess':_assgin_scan_axis})
     else:
         kwargs.update({'preprocess':preprocess})
 
-    ds = xr.open_mfdataset(filePath, **kwargs)
+    ds = xr.open_mfdataset(fullFilePath, **kwargs)
 
     newDimKey = np.append(['x', 'y', 'z'], [ chr(i) for i in range(97, 97+23)])
 

ToolFunction/ToolFunction.py

@@ -1,7 +1,11 @@
-import numpy as np
 import glob
 from datetime import date
 
+import numpy as np
+from uncertainties import unumpy as unp
+
+import xarray as xr
+
 
 def get_mask(dataArray):
     return np.ones(dataArray.shape, dtype=bool)
@@ -41,8 +45,35 @@ def get_date():
     return today.strftime("%y/%m/%d")
 
 
-def resolve_fit_result(fitResult):
-    
+def _combine_uncertainty(value, std):
+    return unp.uarray(value, std)
+
+
+def combine_uncertainty(value, std, dask='parallelized', **kwargs):
+
+    kwargs.update(
+            {
+                "dask": dask,
+            }
+        )
+
+    return xr.apply_ufunc(_combine_uncertainty, value, std, **kwargs)
+
     
+def _seperate_uncertainty_single(data):
+    return data.n, data.s
+
+def _seperate_uncertainty(data):
+    func = np.vectorize(_seperate_uncertainty_single)
+    return func(data)
+
+def seperate_uncertainty(data, dask='parallelized', **kwargs):
     
-    return
+    kwargs.update(
+            {
+                "dask": dask,
+                "output_core_dims": [[], []],
+            }
+        )
+
+    return xr.apply_ufunc(_seperate_uncertainty, data, **kwargs)