toughanimator 0.1.2__tar.gz → 0.1.4__tar.gz

{toughanimator-0.1.2 → toughanimator-0.1.4}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toughanimator
-Version: 0.1.2
+Version: 0.1.4
 Summary: A tool for visualizing TOUGH simulation outputs.
 Home-page: https://github.com/scarletref/toughanimator
 Author: Your Name

{toughanimator-0.1.2 → toughanimator-0.1.4}/setup.py

@@ -2,7 +2,7 @@ from setuptools import setup, find_packages
 
 setup(
     name='toughanimator',  # Package name on PyPI
-    version='0.1.2',
+    version='0.1.4',
     description='A tool for visualizing TOUGH simulation outputs.',
     long_description=open('README.md').read(),
     long_description_content_type='text/markdown',

{toughanimator-0.1.2 → toughanimator-0.1.4}/toughanimator/tough_classes.py

@@ -7,8 +7,8 @@ import numpy as np
 import pandas as pd
 from vtkmodules.all import *
 import pathlib
-import pyvista as pv
 import json
+
 from enum import Enum
 
 class MeshType(Enum):
@@ -69,7 +69,7 @@ class VisVariable:
         }
 
 class VisSetting:
-    def __init__(self, input_file_paths, out_file_paths, vis_dir, corners_file="unkown", out_format_type=OutType.Unknown, tough_version = ToughVersion.Unknown, vis_types=[VisType.ParaView, VisType.Tecplot], mesh_type=MeshType.RegularGrid, debug=False, eos="ECO2N"):
+    def __init__(self, input_file_paths, out_file_paths, vis_dir, corners_file="unkown", out_format_type=OutType.Unknown, tough_version = ToughVersion.Unknown, vis_types=[VisType.ParaView, VisType.Tecplot], mesh_type=MeshType.RegularGrid, debug=False, eos="ECO2N", minc=False):
         self.mesh_type = mesh_type
         self.out_format_type = out_format_type
         self.vis_types = vis_types
@@ -84,7 +84,7 @@ class VisSetting:
         self.corners_file = corners_file
         self.debug = debug
         self.eos = eos
-        self.minc = False
+        self.minc = minc
 
 
     def setBounds(self, x_bounds, y_bounds, z_bounds):
@@ -129,16 +129,21 @@ class vis_reader:
             corners_file = os.path.join(case_dir, config["corners_file"] if "corners_file" in config else "None"),
             debug = config['debug'] if 'debug' in config else False,
             eos = config['EOS'] if 'EOS' in config else "ECO2N",
-            #minc = config['MINC'] if 'MINC' in config else False,
+            minc = config['MINC'] if 'MINC' in config else False,
         )
 
+        # check if the project is using MINC
+        minc_file = os.path.join(case_dir, 'MINC')
+        if os.path.exists(minc_file):
+            setting.minc = True
+        if minc_file in setting.input_file_paths:
+            setting.input_file_paths.remove(minc_file)
+
         for input_file_path in setting.input_file_paths:
             if not os.path.exists(input_file_path):
                 print(f'Can\'t find input file: ({input_file_path}). please check the path or remove it from the config.json.')
                 sys.exit(1)
-            # check if this project use MINC
-            elif input_file_path.endswith('MINC'):
-                setting.minc = True
+
         for out_file_path in setting.out_file_paths:
             if not os.path.exists(input_file_path):
                 print(f'Can\'t find output file: ({out_file_path}). please check the path or remove it from the config.json.')
@@ -429,92 +434,77 @@ class vis_reader:
         self.__write_vtk_file(self.incon_vtk, self.incon_path)
         print(f'    ✓ Initial condition file created: {self.incon_path}')
 
+
+
     def __read_TOUGH2_CSV_outfile(self):
-        output_buffer = io.StringIO()
-        current_time_step = None
-        tim_step_counter = 1
+        self.time_steps_list = []
+        value_type = ValueType.Unknown
+        current_time = None
+        buffer = io.StringIO()
         csv_headers = []
         line_number = -1
-        reading_number = 0
-        value_type = ValueType.Unknown
         start_index = -1
-        self.time_steps_list = []
+        def process_chunk():
+            """Define what to do with each flushed chunk."""
+            buffer.seek(0)
+            df = pd.read_csv(buffer)
+            #print(f"Processing time group:\n{df.head()}")
+            time_step = VisTimeStep(
+                time=float(current_time),
+                time_step=len(self.time_steps_list)+1,
+                iteration=1
+            )
+            self.time_steps_list.append(time_step)
+            if value_type == ValueType.Scalar:
+                self.__write_scalar_result(time_step, df, csv_headers)
+            elif value_type == ValueType.Vector:
+                self.__write_vector_result(time_step, df, csv_headers)
+            
+            buffer.close()
+
         with open(self.current_out_file) as f:
             for line in f:
                 line_number = line_number + 1
                 values = line.strip().split(',')
+
                 if line_number == 0:
                     csv_headers = [x.strip() for x in values]
                     if 'ELEM' in csv_headers and 'INDEX' in csv_headers:
                         value_type = ValueType.Scalar
-                        start_index = 3
-                        
+                        start_index = 1 # remove the first item
+
                     elif 'ELEM1' in csv_headers and 'ELEM2' in csv_headers:
                         value_type = ValueType.Vector
                         start_index = 4
-            
+
+                    # remove the first "TIME" header (to reduce the number of columns)    
                     csv_headers = csv_headers[start_index:]
-                    print(f'    Value type: {value_type.name}')
+
+                    # Write header once
+                    buffer.write(','.join(csv_headers) + '\n')
                     continue
 
-                time = self.__parse_float(values[0].strip())
+                row_time = self.__parse_float(values[0].strip())
 
-                # next time step
-                if current_time_step == None or time != current_time_step.time:
-                    
-                    # when all items in this timestep have been read
-                    if value_type == ValueType.Scalar and reading_number == self.number_of_elements:
-                        output_buffer.seek(0)
-                        df = pd.read_csv(output_buffer, sep=',', header=0)
-                        
-                        self.__write_scalar_result(
-                             current_time_step, df, csv_headers)
-                        output_buffer.flush()
-                        output_buffer.close()
-                        output_buffer = io.StringIO()
-                        reading_number = 0
-                    if value_type == ValueType.Vector and reading_number == self.number_of_connections:
-                        output_buffer.seek(0)
-                        df = pd.read_csv(output_buffer, sep=',', header=0)
-                        #df.to_csv(os.path.join(self.setting.vis_dir, "timestep.csv"), index=False)
-                        self.__write_vector_result(
-                            current_time_step, df, csv_headers)
-                        output_buffer.flush()
-                        output_buffer.close()
-                        output_buffer = io.StringIO()
-                        reading_number = 0
+                if current_time is None:
+                    current_time = row_time
 
-                    current_time_step = VisTimeStep(
-                        time=float(time),
-                        time_step=tim_step_counter,
-                        iteration=1
-                    )
-                    #print(f'    Reading step {current_time_step.time_step_id} : {current_time_step.time} ...')
+                if row_time != current_time:
+                    # Time changed → flush and reset
+                    process_chunk()
+                    buffer = io.StringIO()
+                    buffer.write(','.join(csv_headers) + '\n')  # Write header
+                    current_time = row_time
+
+                # Write current row
+                buffer.write(','.join(values[start_index:]) + '\n')
+            
+            # Flush the last group
+            if buffer.tell() > 0:
+                process_chunk()
+    
 
-                    # Initialize buffer
-                    header_string = ','.join(csv_headers)
-                    output_buffer.write(header_string + '\n')
-                    self.time_steps_list.append(current_time_step)
-                    tim_step_counter = tim_step_counter + 1
-                    
-                    output_buffer.write(','.join(values[start_index:]) + '\n')
-                    reading_number = reading_number + 1
-                else:
-                    output_buffer.write(','.join(values[start_index:]) + '\n')
-                    reading_number = reading_number + 1
-            else:
-                # write the last time step
-                if value_type == ValueType.Scalar:
-                    output_buffer.seek(0)
-                    df = pd.read_csv(output_buffer, sep=',', header=0)
-                    self.__write_scalar_result(current_time_step, df, csv_headers)
-                if value_type == ValueType.Vector:
-                    output_buffer.seek(0)
-                    df = pd.read_csv(output_buffer, sep=',', header=0)
-                    self.__write_vector_result(current_time_step, df, csv_headers)
-                output_buffer.close()    
 
-    # TODO: find whick case is TOUGH3
     def __read_TOUGH3_CSV_outfile(self):
         scalar_buffer = io.StringIO()
         current_time_step = None
@@ -801,7 +791,8 @@ class vis_reader:
 
         
     def __write_scalar_result(self, vis_time_step, dataframe, headers):
-        #print(f'    Writting step {vis_time_step.time_step}: {vis_time_step.time} ...')
+
+
         index = self.time_steps_list.index(vis_time_step)
         #vtr_path = os.path.join(self.setting.vis_dir, 'paraview', f'time_step_{vis_time_step.time_step}.vtr')
 
@@ -811,10 +802,6 @@ class vis_reader:
         #scalar_vtr = vtkRectilinearGrid()
 
         if not os.path.exists(vtr_path):
-            #vtr_reader = vtkXMLRectilinearGridReader()
-            #vtr_reader.SetFileName(self.main_geometry)
-            #vtr_reader.Update()
-            #scalar_vtr = vtr_reader.GetOutput()
             scalar_vtr = self.__read_vtk_file(self.main_geometry)
 
             # add time step data
@@ -833,6 +820,17 @@ class vis_reader:
         vtr = scalar_vtr
 
         variable_list = []
+
+        # make sure to drop TIME and INDEX columns if they exist
+        if 'INDEX' in dataframe.columns:
+            dataframe = dataframe.drop(columns=['INDEX'])
+            headers.remove('INDEX')
+        if 'ELEM' in dataframe.columns:
+            # remove leading spaces from ELEM column
+            dataframe['ELEM'] = dataframe['ELEM'].str.lstrip()
+            headers.remove('ELEM')
+                        
+        # create vtkDoubleArray for each header
         for header in headers:
             array = vtkDoubleArray()
             array.SetName(header)
@@ -840,13 +838,20 @@ class vis_reader:
             variable_list.append(VisVariable(header, ValueType.Scalar, 1))
 
 
+        #if self.setting.minc:
+            #print(f'    MinC is enabled. Adding MinC values to the result.')
+            
         for i in range(0, vtr.GetNumberOfCells()):
+            elemID = self.elemIDArray.GetValue(i)
             index = self.sequence_dist[i]
+            if 'ELEM' in dataframe.columns:
+                index = dataframe['ELEM'].tolist().index(elemID)
             for header in headers:
-                value = float(self.__parse_float(dataframe[header][index]))
+                value = float(self.__parse_float(dataframe[header].iloc[index]))
                 vtr.GetCellData().GetArray(header).InsertNextValue(value)
 
 
+
         # update the variable list
         if self.current_out_file not in self.variable_list:
             self.variable_list[self.current_out_file] = variable_list
@@ -910,6 +915,7 @@ class vis_reader:
         # Other data
         for header in headers:
             array = vtr.GetCellData().GetArray(header)
+
             for e in range(0, vtr.GetNumberOfCells()):
                 file.write(str(array.GetValue(e)) + " ")
             file.write(" \n")
@@ -1152,6 +1158,8 @@ class vis_reader:
             matArray.InsertNextValue(elem_df['MA12'][i])
             matIDArray.InsertNextValue(mat_mapping[elem_df['MA12'][i]])
             pmxArray.InsertNextValue(self.__parse_float(elem_df['PMX'][i]))
+        
+        self.elemIDArray = elemIDArray
 
         '''
         compute permeability
@@ -1275,7 +1283,7 @@ class vis_reader:
 
         d1_array = elem_conne_vtu.GetCellData().GetArray('D1')
         d2_array = elem_conne_vtu.GetCellData().GetArray('D2')
-        elemIDArray = elem_conne_vtu.GetPointData().GetArray('ELEME')
+        #elemIDArray = elem_conne_vtu.GetPointData().GetArray('ELEME')
         volxArray = elem_conne_vtu.GetPointData().GetArray('VOLX')
         matArray = elem_conne_vtu.GetPointData().GetArray('Material')
         matIDArray = elem_conne_vtu.GetPointData().GetArray('Material_ID')
@@ -1496,7 +1504,7 @@ class vis_reader:
             rGrid.SetXCoordinates(xyz_coords_array[0])
             rGrid.SetYCoordinates(xyz_coords_array[1])
             rGrid.SetZCoordinates(xyz_coords_array[2])
-            rGrid.GetCellData().AddArray(elemIDArray)
+            rGrid.GetCellData().AddArray(self.elemIDArray)
             rGrid.GetCellData().AddArray(volxArray)
             rGrid.GetCellData().AddArray(matArray)
 
@@ -1535,7 +1543,7 @@ class vis_reader:
                         vts_points.InsertNextPoint(x, y, z_value)
             
             vts.SetPoints(vts_points) 
-            vts.GetCellData().AddArray(elemIDArray)
+            vts.GetCellData().AddArray(self.elemIDArray)
             vts.GetCellData().AddArray(volxArray)
             vts.GetCellData().AddArray(matArray)
 
@@ -1584,7 +1592,7 @@ class vis_reader:
             # TODO: compute mesh quality and fix bad cells
             
             
-            auto_corner_vtu.GetCellData().AddArray(elemIDArray)
+            auto_corner_vtu.GetCellData().AddArray(self.elemIDArray)
             auto_corner_vtu.GetCellData().AddArray(volxArray)
             auto_corner_vtu.GetCellData().AddArray(matArray)
             if self.rock_dict is not None:
@@ -1923,13 +1931,13 @@ class vis_reader:
                 main_geometray.InsertNextCell(VTK_POLYHEDRON, polyhedron_faces_idlist)
                 
 
-            main_geometray.GetCellData().AddArray(elemIDArray)
+            main_geometray.GetCellData().AddArray(self.elemIDArray)
             main_geometray.GetCellData().AddArray(volxArray)
             main_geometray.GetCellData().AddArray(matArray)
             if self.rock_dict is not None:
                 main_geometray.GetCellData().AddArray(per_array)
                 main_geometray.GetCellData().AddArray(sgr_array)
-            main_geometray.GetCellData().AddArray(matIDArray)
+
             main_geometray.GetCellData().AddArray(matIDArray)
             main_geometray.GetCellData().AddArray(horizon_id_array)
             self.main_geometry = os.path.join(

{toughanimator-0.1.2 → toughanimator-0.1.4}/toughanimator.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: toughanimator
-Version: 0.1.2
+Version: 0.1.4
 Summary: A tool for visualizing TOUGH simulation outputs.
 Home-page: https://github.com/scarletref/toughanimator
 Author: Your Name