From 63074fa7cf1ef1e9a65079227b1e15d7b1db7437 Mon Sep 17 00:00:00 2001
From: kolosret <95316526+kolosret@users.noreply.github.com>
Date: Fri, 1 Nov 2024 17:50:25 -0400
Subject: [PATCH 1/5] Add files via upload

---
 chrest/fileinterpolate.py | 198 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 198 insertions(+)
 create mode 100644 chrest/fileinterpolate.py

diff --git a/chrest/fileinterpolate.py b/chrest/fileinterpolate.py
new file mode 100644
index 0000000..8ba1af7
--- /dev/null
+++ b/chrest/fileinterpolate.py
@@ -0,0 +1,198 @@
+# -*- coding: utf-8 -*-
+"""
+Created on Tue Oct 29 11:23:33 2024
+
+@author: rkolo
+"""
+
+# File convert
+#The aim of this file is to convert between two files using nearest nodes
+
+
+import argparse
+import pathlib
+import sys, os
+import pandas
+
+import numpy as np
+import h5py
+import time
+
+from chrestData import ChrestData
+from supportPaths import expand_path
+from scipy.spatial import KDTree
+
+
+class Fieldconvert:
+    """
+    Creates a new class from hdf5 chrest formatted file(s).
+    """
+
+    def __init__(self):
+
+        self.dimension=0
+        
+        self.SSfilePath=[]
+        self.cellSS=[]
+        self.vertSS=[]
+        self.solSS=[]
+        
+        self.newfilePath=[]
+        self.cellnew=[]
+        self.vertnew=[]
+        self.solnew=[]
+        self.points=[]
+        
+        self.vertindSS=[]
+        self.cellindSS=[]
+
+        self.savedata=False
+        
+    def parsedata(self):
+        
+        hdf5SS = h5py.File(self.SSfilePath, 'r')
+        
+        self.cellSS=hdf5SS['/viz/topology/cells'][()]
+        self.vertSS=hdf5SS['/geometry/vertices'][()]
+        self.solSS=hdf5SS['/fields/solution'][()]
+        self.dimensionSS=self.vertSS.shape[1]
+        hdf5SS.close()
+        
+        hdf5new = h5py.File(self.newfilePath, 'r')
+        self.cellnew=hdf5new['/viz/topology/cells'][()]
+        self.vertnew=hdf5new['/geometry/vertices'][()]
+        self.solnew=hdf5new['/fields/solution'][()]
+        self.dimensionnew=self.vertnew.shape[1]
+        hdf5new.close()
+        
+        
+        self.vertindSS=np.zeros([len(self.vertSS),1])
+        self.cellindSS=np.zeros([len(self.cellSS),1])
+        self.newmat=[]
+        
+        self.serial=True
+        
+        return 0
+    
+    def compute_cell_centers(self,cells,vertices, dimensions=-1):
+        # create a new np array based upon the dim
+        number_cells = cells.shape[0]
+        # vertices = vertices[:]
+        vertices_dim = 1
+        if len(vertices.shape) > 1:
+            vertices_dim = vertices.shape[1]
+        if dimensions < 0:
+            dimensions = vertices_dim
+
+        coords = np.zeros((number_cells, dimensions))
+
+        # march over each cell
+        for c in range(len(coords)):
+            cell_vertices = vertices.take(cells[c], axis=0)
+
+            # take the average
+            cell_center = np.sum(cell_vertices, axis=0)
+            cell_center = cell_center / len(cell_vertices)
+
+            # put back
+            coords[c, 0:vertices_dim] = cell_center
+
+        # if this is one d, flatten
+        if dimensions == 1:
+            coords = coords[:, 0]
+
+        return coords
+    
+        
+ 
+    def findcells(self):
+
+        cell_centersSS = self.compute_cell_centers(self.cellSS,self.vertSS[:],self.dimensionSS)
+        cell_centersnew = self.compute_cell_centers(self.cellnew,self.vertnew[:],self.dimensionnew)
+        
+        if cell_centersSS.shape[1] != cell_centersnew.shape[1]:
+            print('The dimensions of the two files dont match. The only thing currently supported is a 3D->3D and 2D->3D 2D->2D')
+        
+            if cell_centersSS.shape[1] == 2 and cell_centersnew.shape[1] == 3:
+                print('SS shape is 2D and new shape is 3D. The code is assuming the 2D mesh is on the xy-plane')
+                b=np.zeros(cell_centersSS.shape[0])
+                cell_centersSS=np.append(cell_centersSS,b.reshape(b.shape[0],1),1)
+                
+        
+        tree = KDTree(cell_centersSS)
+        dist, self.points = tree.query(cell_centersnew, workers=-1)
+            
+        return 0
+
+        
+    def reorder(self):
+        self.newmat=np.zeros_like(self.solnew)
+        for i in range(len(self.cellnew)):
+            print(self.points[i])
+            self.newmat[0,i,:]=self.solSS[0,self.points[i],:]
+        return 0
+    
+    def writedata(self):
+        
+        hdf5new = h5py.File(self.newfilePath, 'r+')
+
+        solnew=hdf5new['/fields/solution'][()]
+        solnew[...] = self.newmat
+        
+        hdf5new['/fields/solution'][()]=self.newmat
+        
+        hdf5new.close()
+
+        
+        hdf5new = h5py.File(self.newfilePath, 'r+')
+        b=hdf5new['/fields/solution'][()]
+        # solnew[...] = self.newmat
+        hdf5new.close()
+        
+        return 0
+    
+
+        
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description='Generate a chrest data file from an ablate file')
+
+    parser.add_argument('--fileSS', dest='fileSS', type=pathlib.Path, required=True,
+                            help='The steady state file path'
+                                 'to supply more than one file.')
+        
+    parser.add_argument('--filenew', dest='filenew', type=pathlib.Path, required=True,
+                            help='The steady state file path'
+                                 'to supply more than one file.')
+    
+    parser.add_argument('--parallel', dest='parallel', action='store_true',
+                        help="running it in parallel",
+                        )
+
+    print("Start reordering the fields")
+    args = parser.parse_args()
+    
+    convert=Fieldconvert()
+    
+    if args.parallel:
+        convert.serial=False
+    
+    convert.SSfilePath=args.fileSS
+    convert.newfilePath=args.filenew
+    
+    #Step 1 parse data
+    convert.parsedata()
+    
+    #Step 2 Calculate the cell centers, make tree, find closest
+    convert.findcells()
+    
+    #Step 3 Check all fields 
+    
+    #Step 4 Reorder the data
+    convert.reorder()
+    
+    #Step 5 Write out files
+    convert.writedata()
+    
+    
+    print("Finished reordering the fields")
\ No newline at end of file

From 291e5e20029c98b00bb3c98f7363b19b61255a45 Mon Sep 17 00:00:00 2001
From: kolosret <95316526+kolosret@users.noreply.github.com>
Date: Sat, 2 Nov 2024 12:40:23 -0400
Subject: [PATCH 2/5] Adding fixes for 2D->3D, check for mechanisms

---
 chrest/fileinterpolate.py | 106 +++++++++++++++++++++++++-------------
 1 file changed, 69 insertions(+), 37 deletions(-)

diff --git a/chrest/fileinterpolate.py b/chrest/fileinterpolate.py
index 8ba1af7..516c50a 100644
--- a/chrest/fileinterpolate.py
+++ b/chrest/fileinterpolate.py
@@ -11,15 +11,9 @@
 
 import argparse
 import pathlib
-import sys, os
-import pandas
-
+from sys import exit
 import numpy as np
 import h5py
-import time
-
-from chrestData import ChrestData
-from supportPaths import expand_path
 from scipy.spatial import KDTree
 
 
@@ -55,6 +49,17 @@ def parsedata(self):
         self.cellSS=hdf5SS['/viz/topology/cells'][()]
         self.vertSS=hdf5SS['/geometry/vertices'][()]
         self.solSS=hdf5SS['/fields/solution'][()]
+        self.speciesSS = [None] * hdf5SS['/cell_fields/solution_densityYi'].shape[2]
+        # Determine the species
+        for k in hdf5SS['/cell_fields/solution_densityYi'].attrs.keys():
+            print(f"{k} => {hdf5SS['/cell_fields/solution_densityYi'].attrs[k]}")
+            if isinstance(hdf5SS['/cell_fields/solution_densityYi'].attrs[k],np.bytes_):
+                #get the order right...
+                if k[0:13]=='componentName':
+                    idx=''.join(filter(lambda i: i.isdigit(), k))
+                    self.speciesSS[int(idx)]=hdf5SS['/cell_fields/solution_densityYi'].attrs[k].decode('UTF-8')
+        
+        
         self.dimensionSS=self.vertSS.shape[1]
         hdf5SS.close()
         
@@ -62,16 +67,48 @@ def parsedata(self):
         self.cellnew=hdf5new['/viz/topology/cells'][()]
         self.vertnew=hdf5new['/geometry/vertices'][()]
         self.solnew=hdf5new['/fields/solution'][()]
+        self.speciesnew = [None] * hdf5new['/cell_fields/solution_densityYi'].shape[2]
+        # Determine the species
+        for k in hdf5new['/cell_fields/solution_densityYi'].attrs.keys():
+            print(f"{k} => {hdf5new['/cell_fields/solution_densityYi'].attrs[k]}")
+            if isinstance(hdf5new['/cell_fields/solution_densityYi'].attrs[k],np.bytes_):
+                #get the order right...
+                if k[0:13]=='componentName':
+                    idx=''.join(filter(lambda i: i.isdigit(), k))
+                    self.speciesnew[int(idx)]=hdf5new['/cell_fields/solution_densityYi'].attrs[k].decode('UTF-8')
         self.dimensionnew=self.vertnew.shape[1]
         hdf5new.close()
         
-        
-        self.vertindSS=np.zeros([len(self.vertSS),1])
-        self.cellindSS=np.zeros([len(self.cellSS),1])
         self.newmat=[]
         
-        self.serial=True
-        
+        #checking if the mechanisms are the same
+        self.samemech=True
+        for i,x in enumerate(self.speciesSS):
+            self.samemech=x==self.speciesnew[i]
+            
+            
+        #TODO change this in the future at some point...
+        if not self.samemech:
+            raise Exception("I can only do the same mechnisms for now...")
+            exit()
+            
+        if self.dimensionSS != self.dimensionnew:
+            print('The dimensions of the two files dont match. The only thing currently supported is a 3D->3D and 2D->3D 2D->2D')
+            
+            if self.dimensionSS ==3:
+                raise Exception('The steady state file has 3 dimensions')
+                exit()
+            else:
+                self.addzmom=True
+            
+        if (self.dimensionSS+2+len(self.speciesSS)!=self.solSS.shape[2]):
+            raise Exception('You got extra variables in the SS files bubba...')
+            exit()
+
+        if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]):
+            raise Exception('You got extra variables in the new files bubba...')
+            exit()
+
         return 0
     
     def compute_cell_centers(self,cells,vertices, dimensions=-1):
@@ -102,22 +139,18 @@ def compute_cell_centers(self,cells,vertices, dimensions=-1):
             coords = coords[:, 0]
 
         return coords
-    
         
- 
     def findcells(self):
 
         cell_centersSS = self.compute_cell_centers(self.cellSS,self.vertSS[:],self.dimensionSS)
         cell_centersnew = self.compute_cell_centers(self.cellnew,self.vertnew[:],self.dimensionnew)
         
         if cell_centersSS.shape[1] != cell_centersnew.shape[1]:
-            print('The dimensions of the two files dont match. The only thing currently supported is a 3D->3D and 2D->3D 2D->2D')
         
             if cell_centersSS.shape[1] == 2 and cell_centersnew.shape[1] == 3:
                 print('SS shape is 2D and new shape is 3D. The code is assuming the 2D mesh is on the xy-plane')
                 b=np.zeros(cell_centersSS.shape[0])
-                cell_centersSS=np.append(cell_centersSS,b.reshape(b.shape[0],1),1)
-                
+                cell_centersSS=np.append(cell_centersSS,b.reshape(b.shape[0],1),1)           
         
         tree = KDTree(cell_centersSS)
         dist, self.points = tree.query(cell_centersnew, workers=-1)
@@ -127,10 +160,20 @@ def findcells(self):
         
     def reorder(self):
         self.newmat=np.zeros_like(self.solnew)
-        for i in range(len(self.cellnew)):
-            print(self.points[i])
-            self.newmat[0,i,:]=self.solSS[0,self.points[i],:]
-        return 0
+        
+        if self.addzmom:
+            for i in range(len(self.cellnew)):
+                # print(self.points[i])
+                #assume z momentum is 0
+                self.newmat[0,i,:]=np.insert(self.solSS[0,self.points[i],:],4,0)
+            return 0
+        else:
+            #for simple 3D->3D same mechanism
+            for i in range(len(self.cellnew)):
+                # print(self.points[i])
+                self.newmat[0,i,:]=self.solSS[0,self.points[i],:]
+            return 0
+
     
     def writedata(self):
         
@@ -142,18 +185,10 @@ def writedata(self):
         hdf5new['/fields/solution'][()]=self.newmat
         
         hdf5new.close()
-
-        
-        hdf5new = h5py.File(self.newfilePath, 'r+')
-        b=hdf5new['/fields/solution'][()]
-        # solnew[...] = self.newmat
-        hdf5new.close()
-        
+      
         return 0
     
 
-        
-
 if __name__ == "__main__":
     parser = argparse.ArgumentParser(description='Generate a chrest data file from an ablate file')
 
@@ -185,14 +220,11 @@ def writedata(self):
     
     #Step 2 Calculate the cell centers, make tree, find closest
     convert.findcells()
-    
-    #Step 3 Check all fields 
-    
-    #Step 4 Reorder the data
+        
+    #Step 3 Reorder the data
     convert.reorder()
     
-    #Step 5 Write out files
+    #Step 4 Write out files
     convert.writedata()
     
-    
-    print("Finished reordering the fields")
\ No newline at end of file
+    print("Finished reordering the fields")

From ed1e1286badcd1e1f4a164795e09fefaef462e2f Mon Sep 17 00:00:00 2001
From: kolosret <95316526+kolosret@users.noreply.github.com>
Date: Wed, 13 Nov 2024 08:51:11 -0500
Subject: [PATCH 3/5] Fixing issues with extra variables

Now the fileinterpolate file allows for extra variables as long as both files has them
---
 chrest/fileinterpolate.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

diff --git a/chrest/fileinterpolate.py b/chrest/fileinterpolate.py
index 516c50a..014ac0a 100644
--- a/chrest/fileinterpolate.py
+++ b/chrest/fileinterpolate.py
@@ -105,9 +105,10 @@ def parsedata(self):
             raise Exception('You got extra variables in the SS files bubba...')
             exit()
 
-        if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]):
-            raise Exception('You got extra variables in the new files bubba...')
+        if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) == (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) :
+            raise Exception('Only one file has extra variables bubba...')
             exit()
+            
 
         return 0
     

From bd130f0a1f80afce5784cc0ae3faaafbf1e4c2fa Mon Sep 17 00:00:00 2001
From: kolosret <95316526+kolosret@users.noreply.github.com>
Date: Wed, 13 Nov 2024 08:53:29 -0500
Subject: [PATCH 4/5] bigfix in fileinterpolate

---
 chrest/fileinterpolate.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/chrest/fileinterpolate.py b/chrest/fileinterpolate.py
index 014ac0a..61c4db0 100644
--- a/chrest/fileinterpolate.py
+++ b/chrest/fileinterpolate.py
@@ -101,12 +101,8 @@ def parsedata(self):
             else:
                 self.addzmom=True
             
-        if (self.dimensionSS+2+len(self.speciesSS)!=self.solSS.shape[2]):
-            raise Exception('You got extra variables in the SS files bubba...')
-            exit()
-
         if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) == (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) :
-            raise Exception('Only one file has extra variables bubba...')
+            raise Exception('Only one of the files has extra variables bubba...')
             exit()
             
 

From ace9993064ac76585fd2e0a6ff8483d4c8f56c2e Mon Sep 17 00:00:00 2001
From: kolosret <95316526+kolosret@users.noreply.github.com>
Date: Wed, 13 Nov 2024 09:10:00 -0500
Subject: [PATCH 5/5] More Bugfixes

---
 chrest/fileinterpolate.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/chrest/fileinterpolate.py b/chrest/fileinterpolate.py
index 61c4db0..5d14916 100644
--- a/chrest/fileinterpolate.py
+++ b/chrest/fileinterpolate.py
@@ -39,7 +39,8 @@ def __init__(self):
         
         self.vertindSS=[]
         self.cellindSS=[]
-
+        
+        self.addzmom=False
         self.savedata=False
         
     def parsedata(self):
@@ -100,12 +101,11 @@ def parsedata(self):
                 exit()
             else:
                 self.addzmom=True
-            
-        if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) == (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) :
+
+        if (self.dimensionnew+2+len(self.speciesnew)!=self.solnew.shape[2]) != (self.dimensionSS+2+len(self.speciesSS)!=self.solSS.shape[2]) :
             raise Exception('Only one of the files has extra variables bubba...')
             exit()
             
-
         return 0
     
     def compute_cell_centers(self,cells,vertices, dimensions=-1):