Fixed a save glitch, PCA updates

alsinmr · Mar 22, 2024 · 0beb1a0 · 0beb1a0
1 parent 217ce35
commit 0beb1a0
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Showing 6 changed files with 1,295 additions and 3 deletions.
diff --git a/.temp.xtc_offsets.npz b/.temp.xtc_offsets.npz
diff --git a/Fitting/fit.py b/Fitting/fit.py
@@ -349,6 +349,7 @@ def model_free(data,nz:int=None,fixz:list=None,fixA:list=None,Niter:int=None,inc
 
 
     op_in_rho=not(data.source.Type=='NMR')  #Order parameter adds to detector responses (order parameter in rho)
+    # op_in_rho=False
     if op_in_rho and np.any(data.sens.rhoz[:,-1]>0.99):
         op_loc=np.argwhere(data.sens.rhoz[:,-1]>0.99)[0,-1]
     else:
@@ -398,9 +399,11 @@ def model_free(data,nz:int=None,fixz:list=None,fixA:list=None,Niter:int=None,inc
                         A00.append((pinv.T*DelR).sum(1))
                         A00[-1][A00[-1]<0]=0
                         A00[-1][A00[-1]>1]=1
+
                         err.append(((DelR.T-m.T*A00[-1])**2).sum(0))
                     err=np.array(err)
                     i=err.argmin(0)
+
                     A00=np.array(A00).T
                     A[k]=np.array([A00[k][i0] for k,i0 in enumerate(i)])
                     z[k]=zswp[i]
@@ -433,6 +436,7 @@ def model_free(data,nz:int=None,fixz:list=None,fixA:list=None,Niter:int=None,inc
         Rc+=(linear_ex(data.sens.z,data.sens.rhoz.T,z[m]).T*A[m]).T
     z,A=np.array(z),np.array(A)
     if op_in_rho:
+        A[:,A.sum(0)>1]/=A[:,A.sum(0)>1].sum(0)
         Rc+=np.atleast_2d((1-A.sum(0))).T@np.atleast_2d(data.sens.rhoz[:,-1])
 
     out=copy(data)

diff --git a/PCA/PCAsubs.py b/PCA/PCAsubs.py
@@ -78,10 +78,12 @@ def tc_avg(self):
             DESCRIPTION.
 
         """
+
         if self._tcavg is None:
+            dt=self.t[1]
             i=np.argmax(self.Ct<0,axis=1)
-            self._tcavg=np.array([(Ct[:i0]).sum() for Ct,i0 in zip(self.Ct,i)],dtype=np.float64)
-            self._tcavg+=np.arange(len(self._tcavg))*1e-12
+            self._tcavg=np.array([(Ct[:i0]).sum()*dt for Ct,i0 in zip(self.Ct,i)],dtype=np.float64)
+            self._tcavg+=np.arange(len(self._tcavg))*1e-12 #Enforce unique values
         return self._tcavg
 
     @property
@@ -1027,6 +1029,8 @@ def _find(self,key,status='proc'):
     def _raw(self,key):
         """
         Exports a matrix of correlation functions to a data object
+        
+        
 
         Parameters
         ----------

diff --git a/PCA/testPCA.py b/PCA/testPCA.py
@@ -18,6 +18,10 @@
                       traj_files='/Users/albertsmith/Documents/Dynamics/MDsims.nosync/Y1/apo1.xtc',
                       step=1,t0=5900,tf=19150)
 
+select=pyDR.MolSelect(topo='/Volumes/My Book/Y1/apo/prot.pdb',
+                      traj_files='/Volumes/My Book/Y1/apo/apo1.xtc',
+                      step=1,t0=5900,tf=19150)
+
 
 pca=PCA(select)
 pca.select_bond('15N')

diff --git a/Project/Project.py b/Project/Project.py
@@ -235,7 +235,11 @@ def save(self,i='all',include_rawMD=False):
                         src_fname=os.path.abspath(src_data)
                 else:
                     if src_data in self.data_objs:
-                        src_fname=os.path.join(self.directory,self.saved_files[self.data_objs.index(src_data)])
+                        file=self.saved_files[self.data_objs.index(src_data)]
+                        if file is None:
+                            src_fname=None
+                        else:
+                            src_fname=os.path.join(self.directory,)
                     else:
                         src_fname=None