automatic phase correction fixes

ludwigc · Dec 9, 2024 · a2b2f61 · a2b2f61
1 parent f9f52ff
commit a2b2f61
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Showing 2 changed files with 16 additions and 6 deletions.
diff --git a/metabolabpy/nmr/nmrData.py b/metabolabpy/nmr/nmrData.py
@@ -582,9 +582,11 @@ def autophase1d_bl(self, upper_min=10.0, lower_max=-0.5, ref_spc=[], run_compare
         if len(ref_spc) == 0:
             return
 
+        print('autophase1d_bl!!!!!!!')
         phase = [0.0, 0.0]
         #self.autophase1d()
         pars0 = [self.proc.ph0[0], self.proc.ph1[0]]
+        self.proc_spc1d()
         self.auto_ref()
         eval_parameters = optimize.minimize(self.autophase1d_bl_fct, phase, method='Powell',
                                         args=(upper_min, lower_max, ref_spc))
@@ -594,6 +596,7 @@ def autophase1d_bl(self, upper_min=10.0, lower_max=-0.5, ref_spc=[], run_compare
         if run_compare:
             self.autophase1d1()
             self.auto_ref()
+            self.proc_spc1d()
             eval_parameters = optimize.minimize(self.autophase1d_bl_fct, phase, method='Powell',
                                                 args=(upper_min, lower_max, ref_spc))
 
@@ -609,17 +612,18 @@ def autophase1d_bl(self, upper_min=10.0, lower_max=-0.5, ref_spc=[], run_compare
             self.proc.ph0[0] += pars1[0]
             self.proc.ph1[0] += pars1[1]
 
+        self.auto_ref()
         self.proc_spc1d()
-        print(self.proc.window_type[0])
+        #print(self.proc.window_type[0])
         if self.invert_spc():
             self.proc.ph0[0] += 180.0
             self.proc.ph0[0] %= 360.0
             self.proc.ph0[0] += 180.0
             self.proc.ph0[0] %= 360.0
             self.proc.ph0[0] -= 180.0
 
-        self.proc_spc1d()
         self.auto_ref()
+        self.proc_spc1d()
 
     def autophase1d_bl_fct(self, phase, upper_min=10.0, lower_max=-0.5, ref_spc=[], left_only=False):
         if len(ref_spc) == 0:
@@ -796,6 +800,7 @@ def autophase1d1(self, gamma_factor=1.0):
         self.proc.ph0[0] = 0
         self.proc.ph1[0] = 0
         self.proc_spc1d()
+        self.auto_ref()
         fit_parameters = [0.0, 0.0]
         spc = np.copy(self.spc[0])
         eval_parameters = optimize.minimize(self.autophase1d_fct, fit_parameters, method='Powell')
@@ -1031,6 +1036,9 @@ def autopick_hsqc(self, metabolite_list=[]):
         # end autopick_hsqc
 
     def auto_ref(self, tmsp=True):
+        if tmsp == True:
+            self.ref = 'auto'
+
         if self.ref == 'auto':
             if self.acq.o1 == 0:
                 self.ref_shift[0] = 4.76
@@ -1065,7 +1073,7 @@ def auto_ref(self, tmsp=True):
                     npts = len(self.spc[0])
                     r = np.arange(npts - max(pts), npts - min(pts))
                     r = np.copy(r[np.where(r < len(self.spc[0]))])
-                    spc = self.spc[0][r].real
+                    spc = np.abs(self.spc[0][r].real)
                     ref_p = np.where(spc == np.amax(spc))
                     self.ref_point[0] -= ref_p[0][0] - int((max(pts) - min(pts)) / 2) + 1
                 else:

diff --git a/metabolabpy/nmr/nmrDataSet.py b/metabolabpy/nmr/nmrDataSet.py
@@ -128,27 +128,29 @@ def autophase1d_bl(self, upper_min=10.0, lower_max=-0.5):
             return
 
         if self.e != ref_spc_no:
+            self.nmrdat[self.s][ref_spc_no].proc_spc1d()
             ref_spc = np.copy(self.nmrdat[self.s][ref_spc_no].spc[0])
             self.nmrdat[self.s][self.e].proc.ph0[0] = self.nmrdat[self.s][ref_spc_no].proc.ph0[0]
             self.nmrdat[self.s][self.e].proc.ph1[0] = self.nmrdat[self.s][ref_spc_no].proc.ph1[0]
             self.nmrdat[self.s][self.e].proc_spc1d()
             self.nmrdat[self.s][self.e].auto_ref()
             self.nmrdat[self.s][self.e].autophase1d_bl(upper_min, lower_max, ref_spc)
-            self.auto_ref()
+            self.nmrdat[self.s][self.e].auto_ref()
 
 
     def autophase1d_bl_all(self, upper_min=10.0, lower_max=-0.5):
         ref_spc_no = self.nmrdat[self.s][0].display.ph_ref_exp - 1
         if ref_spc_no == -1:
             return
 
+        self.nmrdat[self.s][ref_spc_no].proc_spc1d()
+        ref_spc = np.copy(self.nmrdat[self.s][ref_spc_no].spc[0])
         for k in range(len(self.nmrdat[self.s])):
             if k != ref_spc_no:
-                ref_spc = np.copy(self.nmrdat[self.s][ref_spc_no].spc[0])
                 self.nmrdat[self.s][k].proc.ph0[0] = self.nmrdat[self.s][ref_spc_no].proc.ph0[0]
                 self.nmrdat[self.s][k].proc.ph1[0] = self.nmrdat[self.s][ref_spc_no].proc.ph1[0]
-                self.nmrdat[self.s][k].proc_spc1d()
                 self.nmrdat[self.s][k].auto_ref()
+                self.nmrdat[self.s][k].proc_spc1d()
                 self.nmrdat[self.s][k].autophase1d_bl(upper_min, lower_max, ref_spc)
                 self.nmrdat[self.s][k].auto_ref()