def readFormatFile(filename):
""" Read a format file and return a dictionary. The each line of the format file should be of the form:
"variable name" @ file_id -> column_id, file_id -> column_id, ...
It means that the "column_id"-th column(s) of file(s) with "file_id" corresponds to (components of) data with name "variable name". If no "->" is found, then all "file_id" are assumed to be 1. Those lines without "@" will be skipped.
The return dictionary is of the format:
{"variable name": [[file_id, column_id],...]}
"""
# global control_variables
D = {}
for aLine in open(filename):
if "@" not in aLine: # skip those lines without "@":
print(
"vtk_converter::readFormatFile warning: no @ symbol found in the line:\n"
+ aLine + "\n and it will be skipped.\n")
continue
[name, column_mapping] = [x.strip() for x in aLine.split("@")]
if name == "skip":
# this is a control variable
control_variables.to_skip = dict(
[[int(y) for y in stringToNumbers(x, "->")]
for x in column_mapping.split(",")])
else:
D[name] = [[int(y) for y in stringToNumbers(x, "->")]
for x in column_mapping.split(",")]
return D
def convertToVtk(output_file, format_file, file_list, structured="auto"):
""" Convert data given in the list "file_list" to "output_file". The name of "output_file" should contain a "%d" string for time slicing (t=0 if not included). Format of the files are defined in "format_file" (see readFormatFile function). The variable "x", "y", "z" are used to defined (unstructured) grids. The variable "t" is used to slice the data file: everytime its value changes, a new file "output_file % index" will be used for the output.
"""
file_list = FLL([file_list])
# to make it more user friendly: for single file there need no "[]" around it
fmt = readFormatFile(format_file)
# raw format
D = fmtToMapping(fmt)
# regulated format
t_id = 0
# controls the time-slice of the output
# open files
fids = [open(x) for x in file_list]
# skip lines
for skip_fid in control_variables.to_skip.keys():
[
fids[skip_fid - 1].readline()
for i in range(control_variables.to_skip[skip_fid])
] # fid-1 b/c indices start from 0
firstline_flag = 1
[grid, scalars, vectors] = initialDataLists(D)
# grid is the collection of grid points, it is of the form [[x,y,z],...], the missed variables will be set to 0. scalars and vectors are nested lists, they has the format scalars=[[[#,#,...],[#,#,...],...],vectors=[[[#,#,#],[#,#,#],...],...]
aStringLine = [x.readline() for x in fids]
aLine = [stringToNumbers(y, ",") for y in aStringLine]
# read one line from all files, then convert to nested lists. For example, if the 1st file has 2 columns and the 2nd has 1, then aLine will be like [[#,#],[#]]
while aStringLine[
0] != "": # total number of read rows is determined by the number of rows of the first file
if aLine[0] != []: # not a comment-only line
new_time = D["t"](aLine)
if firstline_flag:
old_time = new_time
# skip the 1st line
firstline_flag = 0
# no longer the 1st line
if new_time != old_time: # time step changed!
dumpVtk(output_file % t_id, grid, scalars, vectors, D,
structured)
# output current slice
old_time = new_time
# update current time
[grid, scalars, vectors] = initialDataLists(D)
# clear buffer
fillData(grid, scalars, vectors, D, aLine)
# add newly read line
t_id = t_id + 1
# advance to the next time step
else: # time step kept; keep filling data
fillData(grid, scalars, vectors, D, aLine)
aStringLine = [x.readline() for x in fids]
aLine = [stringToNumbers(y, ",") for y in aStringLine]
# read one line from all files, then convert to nested lists. For example, if the 1st file has 2 columns and the 2nd has 1, then aLine will be like [[#,#],[#]]
dumpVtk(output_file % t_id, grid, scalars, vectors, D, structured)
# the final output
print("Finished. Thanks for using vtk_converter. Zhi Qiu 2011")
def readFormatFile(filename):
""" Read a format file and return a dictionary. The each line of the format file should be of the form:
"variable name" @ file_id -> column_id, file_id -> column_id, ...
It means that the "column_id"-th column(s) of file(s) with "file_id" corresponds to (components of) data with name "variable name". If no "->" is found, then all "file_id" are assumed to be 1. Those lines without "@" will be skipped.
The return dictionary is of the format:
{"variable name": [[file_id, column_id],...]}
"""
# global control_variables
D = {};
for aLine in open(filename):
if "@" not in aLine: # skip those lines without "@":
print("vtk_converter::readFormatFile warning: no @ symbol found in the line:\n"+aLine+"\n and it will be skipped.\n");
continue;
[name, column_mapping] = [x.strip() for x in aLine.split("@")];
if name=="skip":
# this is a control variable
control_variables.to_skip = dict([[int(y) for y in stringToNumbers(x,"->")] for x in column_mapping.split(",")]);
else:
D[name] = [[int(y) for y in stringToNumbers(x,"->")] for x in column_mapping.split(",")];
return D;
def convertToVtk(output_file, format_file, file_list, structured="auto"):
""" Convert data given in the list "file_list" to "output_file". The name of "output_file" should contain a "%d" string for time slicing (t=0 if not included). Format of the files are defined in "format_file" (see readFormatFile function). The variable "x", "y", "z" are used to defined (unstructured) grids. The variable "t" is used to slice the data file: everytime its value changes, a new file "output_file % index" will be used for the output.
"""
file_list = FLL([file_list]); # to make it more user friendly: for single file there need no "[]" around it
fmt = readFormatFile(format_file); # raw format
D = fmtToMapping(fmt); # regulated format
t_id = 0;# controls the time-slice of the output
# open files
fids = [open(x) for x in file_list];
# skip lines
for skip_fid in control_variables.to_skip.keys():
[fids[skip_fid-1].readline() for i in range(control_variables.to_skip[skip_fid])] # fid-1 b/c indices start from 0
firstline_flag = 1;
[grid, scalars, vectors] = initialDataLists(D); # grid is the collection of grid points, it is of the form [[x,y,z],...], the missed variables will be set to 0. scalars and vectors are nested lists, they has the format scalars=[[[#,#,...],[#,#,...],...],vectors=[[[#,#,#],[#,#,#],...],...]
aStringLine = [x.readline() for x in fids];
aLine = [stringToNumbers(y,",") for y in aStringLine]; # read one line from all files, then convert to nested lists. For example, if the 1st file has 2 columns and the 2nd has 1, then aLine will be like [[#,#],[#]]
while aStringLine[0]!="": # total number of read rows is determined by the number of rows of the first file
if aLine[0]!=[]: # not a comment-only line
new_time=D["t"](aLine);
if firstline_flag:
old_time=new_time; # skip the 1st line
firstline_flag=0; # no longer the 1st line
if new_time!=old_time: # time step changed!
dumpVtk(output_file % t_id, grid, scalars, vectors, D, structured); # output current slice
old_time = new_time; # update current time
[grid, scalars, vectors] = initialDataLists(D); # clear buffer
fillData(grid, scalars, vectors, D, aLine); # add newly read line
t_id=t_id+1; # advance to the next time step
else: # time step kept; keep filling data
fillData(grid, scalars, vectors, D, aLine);
aStringLine = [x.readline() for x in fids];
aLine = [stringToNumbers(y,",") for y in aStringLine]; # read one line from all files, then convert to nested lists. For example, if the 1st file has 2 columns and the 2nd has 1, then aLine will be like [[#,#],[#]]
dumpVtk(output_file % t_id, grid, scalars, vectors, D, structured); # the final output
print("Finished. Thanks for using vtk_converter. Zhi Qiu 2011");
