From 9796d0ae22439e4f941af2d8257dd2e1470d88a1 Mon Sep 17 00:00:00 2001
From: Hal Finkel <hfinkel@anl.gov>
Date: Mon, 25 Sep 2017 19:20:08 -0500
Subject: [PATCH] Add support for float4 (and similar) to Python bindings
---
python/example.py | 11 +++++++++--
python/genericio.py | 35 +++++++++++++++++++++-------------
python/lib/gio.cxx | 46 ++++++++++++++++++++++++++++++++-------------
python/lib/gio.h | 20 +++++++++++---------
4 files changed, 75 insertions(+), 37 deletions(-)
diff --git a/python/example.py b/python/example.py
index d4c2d9e..fb5240a 100644
--- a/python/example.py
+++ b/python/example.py
@@ -38,11 +38,18 @@
# *****************************************************************************
import sys
+import numpy as np
import genericio as gio
name = sys.argv[1]
gio.gio_inspect(name)
-x = gio.gio_read(name, "x")
-print x
+if gio.gio_has_variable(name, "x"):
+ x = gio.gio_read(name, "x")
+ y = gio.gio_read(name, "y")
+ z = gio.gio_read(name, "z")
+ print np.column_stack((x, y, z))
+else:
+ pos = gio.gio_read(name, "pos")
+ print pos
diff --git a/python/genericio.py b/python/genericio.py
index 7e94614..c9685e6 100644
--- a/python/genericio.py
+++ b/python/genericio.py
@@ -52,17 +52,20 @@ libpygio.get_elem_num.argtypes=[ct.c_char_p]
libpygio.get_variable_type.restype=ct.c_int
libpygio.get_variable_type.argtypes=[ct.c_char_p,ct.c_char_p]
+libpygio.get_variable_field_count.restype=ct.c_int
+libpygio.get_variable_field_count.argtypes=[ct.c_char_p,ct.c_char_p]
+
libpygio.read_gio_int32.restype=None
-libpygio.read_gio_int32.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int)]
+libpygio.read_gio_int32.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int),ct.c_int]
libpygio.read_gio_int64.restype=None
-libpygio.read_gio_int64.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int64)]
+libpygio.read_gio_int64.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_int64),ct.c_int]
libpygio.read_gio_float.restype=None
-libpygio.read_gio_float.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_float)]
+libpygio.read_gio_float.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_float),ct.c_int]
libpygio.read_gio_double.restype=None
-libpygio.read_gio_double.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_double)]
+libpygio.read_gio_double.argtypes=[ct.c_char_p,ct.c_char_p,ct.POINTER(ct.c_double),ct.c_int]
libpygio.inspect_gio.restype=None
libpygio.inspect_gio.argtypes=[ct.c_char_p]
@@ -70,6 +73,7 @@ libpygio.inspect_gio.argtypes=[ct.c_char_p]
def gio_read(file_name,var_name):
var_size = libpygio.get_elem_num(file_name)
var_type = libpygio.get_variable_type(file_name,var_name)
+ field_count = libpygio.get_variable_field_count(file_name,var_name)
if(var_type==10):
print "Variable not found"
return
@@ -77,25 +81,30 @@ def gio_read(file_name,var_name):
print "variable type not known (not int32/int64/float/double)"
elif(var_type==0):
#float
- result = np.ndarray(var_size,dtype=np.float32)
- libpygio.read_gio_float(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_float)))
+ result = np.ndarray((var_size,field_count),dtype=np.float32)
+ libpygio.read_gio_float(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_float)),field_count)
return result
elif(var_type==1):
#double
- result = np.ndarray(var_size,dtype=np.float64)
- libpygio.read_gio_double(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_double)))
+ result = np.ndarray((var_size,field_count),dtype=np.float64)
+ libpygio.read_gio_double(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_double)),field_count)
return result
elif(var_type==2):
#int32
- result = np.ndarray(var_size,dtype=np.int32)
- libpygio.read_gio_int32(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int32)))
+ result = np.ndarray((var_size,field_count),dtype=np.int32)
+ libpygio.read_gio_int32(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int32)),field_count)
return result
elif(var_type==3):
#int64
- result = np.ndarray(var_size,dtype=np.int64)
- libpygio.read_gio_int64(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int64)))
+ result = np.ndarray((var_size,field_count),dtype=np.int64)
+ libpygio.read_gio_int64(file_name,var_name,result.ctypes.data_as(ct.POINTER(ct.c_int64)),field_count)
return result
-
+
+def gio_has_variable(file_name,var_name):
+ var_size = libpygio.get_elem_num(file_name)
+ var_type = libpygio.get_variable_type(file_name,var_name)
+ return var_type!=10
+
def gio_inspect(file_name):
libpygio.inspect_gio(file_name)
diff --git a/python/lib/gio.cxx b/python/lib/gio.cxx
index 82cebd4..26ea8e3 100644
--- a/python/lib/gio.cxx
+++ b/python/lib/gio.cxx
@@ -42,17 +42,17 @@
#include "gio.h"
#include <iostream>
- void read_gio_float(char* file_name, char* var_name, float* data){
- read_gio<float>(file_name,var_name,data);
+ void read_gio_float(char* file_name, char* var_name, float* data, int field_count){
+ read_gio<float>(file_name,var_name,data,field_count);
}
- void read_gio_double(char* file_name, char* var_name, double* data){
- read_gio<double>(file_name,var_name,data);
+ void read_gio_double(char* file_name, char* var_name, double* data, int field_count){
+ read_gio<double>(file_name,var_name,data,field_count);
}
- void read_gio_int32(char* file_name, char* var_name, int* data){
- read_gio<int>(file_name,var_name,data);
+ void read_gio_int32(char* file_name, char* var_name, int* data, int field_count){
+ read_gio<int>(file_name,var_name,data,field_count);
}
- void read_gio_int64(char* file_name, char* var_name, int64_t* data){
- read_gio<int64_t>(file_name,var_name,data);
+ void read_gio_int64(char* file_name, char* var_name, int64_t* data, int field_count){
+ read_gio<int64_t>(file_name,var_name,data,field_count);
}
int64_t get_elem_num(char* file_name){
@@ -76,13 +76,13 @@
for(int i =0;i<num;++i){
gio::GenericIO::VariableInfo vinfo = VI[i];
if(vinfo.Name == var_name){
- if(vinfo.IsFloat && vinfo.Size == 4)
+ if(vinfo.IsFloat && vinfo.ElementSize == 4)
return float_type;
- else if(vinfo.IsFloat && vinfo.Size == 8)
+ else if(vinfo.IsFloat && vinfo.ElementSize == 8)
return double_type;
- else if(!vinfo.IsFloat && vinfo.Size == 4)
+ else if(!vinfo.IsFloat && vinfo.ElementSize == 4)
return int32_type;
- else if(!vinfo.IsFloat && vinfo.Size == 8)
+ else if(!vinfo.IsFloat && vinfo.ElementSize == 8)
return int64_type;
else
return type_not_found;
@@ -92,6 +92,22 @@
}
+ int get_variable_field_count(char* file_name,char* var_name){
+ gio::GenericIO reader(file_name);
+ std::vector<gio::GenericIO::VariableInfo> VI;
+ reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
+ reader.getVariableInfo(VI);
+
+ int num =VI.size();
+ for(int i =0;i<num;++i){
+ gio::GenericIO::VariableInfo vinfo = VI[i];
+ if(vinfo.Name == var_name) {
+ return vinfo.Size/vinfo.ElementSize;
+ }
+ }
+ return 0;
+ }
+
extern "C" void inspect_gio(char* file_name){
int64_t size = get_elem_num(file_name);
gio::GenericIO reader(file_name);
@@ -109,7 +125,11 @@ extern "C" void inspect_gio(char* file_name){
std::cout<<"[f";
else
std::cout<<"[i";
- std::cout<<" "<<vinfo.Size*8<<"] ";
+ int NumElements = vinfo.Size/vinfo.ElementSize;
+ std::cout<<" "<<vinfo.ElementSize*8;
+ if (NumElements > 1)
+ std::cout<<"x"<<NumElements;
+ std::cout<<"] ";
std::cout<<vinfo.Name<<std::endl;
}
std::cout<<"\n(i=integer,f=floating point, number bits size)"<<std::endl;
diff --git a/python/lib/gio.h b/python/lib/gio.h
index fcfa8cf..2a150ce 100644
--- a/python/lib/gio.h
+++ b/python/lib/gio.h
@@ -45,7 +45,7 @@
#include <sstream>
template <class T>
-void read_gio(char* file_name, std::string var_name, T*& data){
+void read_gio(char* file_name, std::string var_name, T*& data, int field_count){
gio::GenericIO reader(file_name);
reader.openAndReadHeader(gio::GenericIO::MismatchAllowed);
int num_ranks = reader.readNRanks();
@@ -56,23 +56,24 @@ void read_gio(char* file_name, std::string var_name, T*& data){
if(max_size < rank_size[i])
max_size = rank_size[i];
}
- T* rank_data = new T[max_size+reader.requestedExtraSpace()/sizeof(T)];
+ T* rank_data = new T[max_size*field_count+reader.requestedExtraSpace()/sizeof(T)];
int64_t offset =0;
- reader.addVariable(var_name,rank_data,true);
+ reader.addScalarizedVariable(var_name,rank_data,field_count,
+ gio::GenericIO::VarHasExtraSpace);
for(int i=0;i<num_ranks;++i){
reader.readData(i,false);
- std::copy(rank_data,rank_data+rank_size[i],data+offset);
- offset +=rank_size[i];
+ std::copy(rank_data,rank_data+rank_size[i]*field_count,data+offset);
+ offset +=rank_size[i]*field_count;
}
delete [] rank_data;
reader.close();
}
extern "C" int64_t get_elem_num(char* file_name);
-extern "C" void read_gio_float (char* file_name, char* var_name, float* data);
-extern "C" void read_gio_double(char* file_name, char* var_name, double* data);
-extern "C" void read_gio_int32 (char* file_name, char* var_name, int* data);
-extern "C" void read_gio_int64 (char* file_name, char* var_name, int64_t* data);
+extern "C" void read_gio_float (char* file_name, char* var_name, float* data, int field_count);
+extern "C" void read_gio_double(char* file_name, char* var_name, double* data, int field_count);
+extern "C" void read_gio_int32 (char* file_name, char* var_name, int* data, int field_count);
+extern "C" void read_gio_int64 (char* file_name, char* var_name, int64_t* data, int field_count);
enum var_type{
float_type=0,
double_type=1,
@@ -82,4 +83,5 @@ enum var_type{
var_not_found=10
};
extern "C" var_type get_variable_type(char* file_name,char* var_name);
+extern "C" int get_variable_field_count(char* file_name,char* var_name);
extern "C" void inspect_gio(char* file_name);
--
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