I want to read a chunk of data which is just one frame of many frames stored in one dataset. The shape of the whole dataset is (10, 11214,3), 10 frames each frame has 11214 rows and 4 columns. Here is the file. The chunk I want to read would have the shape (11214,3). I can print the predefined array using, but I'm not sure how can I read data from a hdf5 file. Here is my code,
#include <h5xx/h5xx.hpp>
#include <boost/multi_array.hpp>
#include <iostream>
#include <vector>
#include <cstdio>
typedef boost::multi_array<int, 2> array_2d_t;
const int NI=10;
const int NJ=NI;
void print_array(array_2d_t const& array)
{
for (unsigned int j = 0; j < array.shape()[1]; j++)
{
for (unsigned int i = 0; i < array.shape()[0]; i++)
{
printf("%2d ", array[j][i]);
}
printf("\n");
}
}
void write_int_data(std::string const& filename, array_2d_t const& array)
{
h5xx::file file(filename, h5xx::file::trunc);
std::string name;
{
// --- create dataset and fill it with the default array data (positive values)
name = "integer array";
h5xx::create_dataset(file, name, array);
h5xx::write_dataset(file, name, array);
// --- create a slice object (aka hyperslab) to specify the location in the dataset to be overwritten
std::vector<int> offset; int offset_raw[2] = {4,4}; offset.assign(offset_raw, offset_raw + 2);
std::vector<int> count; int count_raw[2] = {2,2}; count.assign(count_raw, count_raw + 2);
h5xx::slice slice(offset, count);
}
}
void read_int_data(std::string const& filename)
{
h5xx::file file(filename, h5xx::file::in);
std::string name = "integer array";
// read and print the full dataset
{
array_2d_t array;
// --- read the complete dataset into array, the array is resized and overwritten internally
h5xx::read_dataset(file, name, array);
printf("original integer array read from file, negative number patch was written using a slice\n");
print_array(array);
printf("\n");
}
}
int main(int argc, char** argv)
{
std::string filename = argv[0];
filename.append(".h5");
// --- do a few demos/tests using integers
{
array_2d_t array(boost::extents[NJ][NI]);
{
const int nelem = NI*NJ;
int data[nelem];
for (int i = 0; i < nelem; i++)
data[i] = i;
array.assign(data, data + nelem);
}
write_int_data(filename, array);
read_int_data(filename);
}
return 0;
}
I'm using the h5xx — a template-based C++ wrapper for the HDF5 library link and boost library.
The datasets are stored in particles/lipids/box/positions path. The dataset name value holds the frames.
argv[0] is not what you want (arguments start at 1, 0 is the program name). Consider bounds checking as well:
std::vector<std::string> const args(argv, argv + argc);
std::string const filename = args.at(1) + ".h5";
the initialization can be done directly, without a temporary array (what is multi_array for, otherwise?)
for (size_t i = 0; i < array.num_elements(); i++)
array.data()[i] = i;
Or indeed, make it an algorithm:
std::iota(array.data(), array.data() + array.num_elements(), 0);
same with vectors:
std::vector<int> offset; int offset_raw[2] = {4,4}; offset.assign(offset_raw, offset_raw + 2);
std::vector<int> count; int count_raw[2] = {2,2}; count.assign(count_raw, count_raw + 2);
besides being a formatting mess can be simply
std::vector offset{4,4}, count{2,2};
h5xx::slice slice(offset, count);
On To The Real Question
The code has no relevance to the file. At all. I created some debug/tracing code to dump the file contents:
void dump(h5xx::group const& g, std::string indent = "") {
auto dd = g.datasets();
auto gg = g.groups();
for (auto it = dd.begin(); it != dd.end(); ++it) {
std::cout << indent << " ds:" << it.get_name() << "\n";
}
for (auto it = gg.begin(); it != gg.end(); ++it) {
dump(*it, indent + "/" + it.get_name());
}
}
int main()
{
h5xx::file xaa("xaa.h5", h5xx::file::mode::in);
dump(xaa);
}
Prints
/particles/lipids/box/edges ds:box_size
/particles/lipids/box/edges ds:step
/particles/lipids/box/edges ds:time
/particles/lipids/box/edges ds:value
/particles/lipids/box/positions ds:step
/particles/lipids/box/positions ds:time
/particles/lipids/box/positions ds:value
Now we can drill down to the dataset. Let's see whether we can figure out the correct type. It certainly is NOT array_2d_t:
h5xx::dataset ds(xaa, "particles/lipids/box/positions/value");
array_2d_t a;
h5xx::datatype detect(a);
std::cout << "type: " << std::hex << ds.get_type() << std::dec << "\n";
std::cout << "detect: " << std::hex << detect.get_type_id() << std::dec << "\n";
Prints
type: 30000000000013b
detect: 30000000000000c
That's a type mismatch. I guess I'll have to learn to read that gibberish as well...
Let's add some diagnostics:
void diag_type(hid_t type)
{
std::cout << " Class " << ::H5Tget_class(type) << std::endl;
std::cout << " Size " << ::H5Tget_size(type) << std::endl;
std::cout << " Sign " << ::H5Tget_sign(type) << std::endl;
std::cout << " Order " << ::H5Tget_order(type) << std::endl;
std::cout << " Precision " << ::H5Tget_precision(type) << std::endl;
std::cout << " NDims " << ::H5Tget_array_ndims(type) << std::endl;
std::cout << " NMembers " << ::H5Tget_nmembers(type) << std::endl;
}
int main()
{
h5xx::file xaa("xaa.h5", h5xx::file::mode::in);
// dump(xaa);
{
h5xx::group g(xaa, "particles/lipids/box/positions");
h5xx::dataset ds(g, "value");
std::cout << "dataset: " << std::hex << ds.get_type() << std::dec << std::endl;
diag_type(ds.get_type());
}
{
array_2d_t a(boost::extents[NJ][NI]);
h5xx::datatype detect(a);
std::cout << "detect: " << std::hex << detect.get_type_id() << std::dec << std::endl;
diag_type(detect.get_type_id());
}
}
Prints
dataset: 30000000000013b
Class 1
Size 4
Sign -1
Order 0
Precision 32
NDims -1
NMembers -1
detect: 30000000000000c
Class 0
Size 4
Sign 1
Order 0
Precision 32
NDims -1
NMembers -1
At least we know that HST_FLOAT (class 1) is required. Let's modify array_2d_t:
using array_2d_t = boost::multi_array<float, 2>;
array_2d_t a(boost::extents[11214][3]);
This at least makes the data appear similarly. Let's ... naively try to read:
h5xx::read_dataset(ds, a);
Oops, that predictably throws
terminate called after throwing an instance of 'h5xx::error'
what(): /home/sehe/Projects/stackoverflow/deps/h5xx/h5xx/dataset/boost_multi_array.hpp:176:read_dataset(): dataset "/particles/lipi
ds/box/positions/value" and target array have mismatching dimensions
No worries, we can guess:
using array_3d_t = boost::multi_array<float, 3>;
array_3d_t a(boost::extents[10][11214][3]);
h5xx::read_dataset(ds, a);
At least this does work. Adapting the print function:
template <typename T> void print_array(T const& array) {
for (auto const& row : array) {
for (auto v : row) printf("%5f ", v);
printf("\n");
}
}
Now we can print the first frame:
h5xx::read_dataset(ds, a);
print_array(*a.begin()); // print the first frame
This prints:
80.480003 35.360001 4.250000
37.450001 3.920000 3.960000
18.530001 -9.690000 4.680000
55.389999 74.339996 4.600000
22.110001 68.709999 3.850000
-4.130000 24.040001 3.730000
40.160000 6.390000 4.730000
-5.400000 35.730000 4.850000
36.669998 22.450001 4.080000
-3.680000 -10.660000 4.180000
(...)
That checks out with h5ls -r -d xaa.h5/particles/lipids/box/positions/value:
particles/lipids/box/positions/value Dataset {75/Inf, 11214, 3}
Data:
(0,0,0) 80.48, 35.36, 4.25, 37.45, 3.92, 3.96, 18.53, -9.69, 4.68,
(0,3,0) 55.39, 74.34, 4.6, 22.11, 68.71, 3.85, -4.13, 24.04, 3.73,
(0,6,0) 40.16, 6.39, 4.73, -5.4, 35.73, 4.85, 36.67, 22.45, 4.08, -3.68,
(0,9,1) -10.66, 4.18, 35.95, 36.43, 5.15, 57.17, 3.88, 5.08, -23.64,
(0,12,1) 50.44, 4.32, 6.78, 8.24, 4.36, 21.34, 50.63, 5.21, 16.29,
(0,15,1) -1.34, 5.28, 22.26, 71.25, 5.4, 19.76, 10.38, 5.34, 78.62,
(0,18,1) 11.13, 5.69, 22.14, 59.7, 4.92, 15.65, 47.28, 5.22, 82.41,
(0,21,1) 2.09, 5.24, 16.87, -11.68, 5.35, 15.54, -0.63, 5.2, 81.25,
(...)
The Home Stretch: Adding The Slice
array_2d_t read_frame(int frame_no) {
h5xx::file xaa("xaa.h5", h5xx::file::mode::in);
h5xx::group g(xaa, "particles/lipids/box/positions");
h5xx::dataset ds(g, "value");
array_2d_t a(boost::extents[11214][3]);
std::vector offsets{frame_no, 0, 0}, counts{1, 11214, 3};
h5xx::slice slice(offsets, counts);
h5xx::read_dataset(ds, a, slice);
return a;
}
There you have it. Now we can print any frame:
print_array(read_frame(0));
Printing the same as before. Let's try the last frame:
print_array(read_frame(9));
Prints
79.040001 36.349998 3.990000
37.250000 3.470000 4.140000
18.600000 -9.270000 4.900000
55.669998 75.070000 5.370000
21.920000 67.709999 3.790000
-4.670000 24.770000 3.690000
40.000000 6.060000 5.240000
-5.340000 36.320000 5.410000
36.369999 22.490000 4.130000
-3.520000 -10.430000 4.280000
(...)
Checking again with h5ls -r -d xaa.h5/particles/lipids/box/positions/value |& grep '(9' | head confirms:
(9,0,0) 79.04, 36.35, 3.99, 37.25, 3.47, 4.14, 18.6, -9.27, 4.9, 55.67,
(9,3,1) 75.07, 5.37, 21.92, 67.71, 3.79, -4.67, 24.77, 3.69, 40, 6.06,
(9,6,2) 5.24, -5.34, 36.32, 5.41, 36.37, 22.49, 4.13, -3.52, -10.43,
(9,9,2) 4.28, 35.8, 36.43, 4.99, 56.6, 4.09, 5.04, -23.37, 49.42, 3.81,
(9,13,0) 6.31, 8.83, 4.56, 22.01, 50.38, 5.43, 16.3, -2.92, 5.4, 22.02,
(9,16,1) 70.09, 5.36, 20.23, 11.12, 5.66, 78.48, 11.34, 6.09, 20.26,
(9,19,1) 61.45, 5.35, 14.25, 48.32, 5.35, 79.95, 1.71, 5.38, 17.56,
(9,22,1) -11.61, 5.39, 15.64, -0.19, 5.06, 80.43, 71.77, 5.29, 75.54,
(9,25,1) 35.14, 5.26, 22.45, 56.86, 5.56, 16.47, 52.97, 6.16, 20.62,
(9,28,1) 65.12, 5.26, 19.68, 71.2, 5.52, 23.39, 49.84, 5.28, 22.7,
Full Listing
#include <boost/multi_array.hpp>
#include <h5xx/h5xx.hpp>
#include <iostream>
using array_2d_t = boost::multi_array<float, 2>;
template <typename T> void print_array(T const& array)
{
for (auto const& row : array) { for (auto v : row)
printf("%5f ", v);
printf("\n");
}
}
void dump(h5xx::group const& g, std::string indent = "") {
auto dd = g.datasets();
auto gg = g.groups();
for (auto it = dd.begin(); it != dd.end(); ++it) {
std::cout << indent << " ds:" << it.get_name() << std::endl;
}
for (auto it = gg.begin(); it != gg.end(); ++it) {
dump(*it, indent + "/" + it.get_name());
}
}
array_2d_t read_frame(int frame_no) {
h5xx::file xaa("xaa.h5", h5xx::file::mode::in);
h5xx::group g(xaa, "particles/lipids/box/positions");
h5xx::dataset ds(g, "value");
array_2d_t arr(boost::extents[11214][3]);
std::vector offsets{frame_no, 0, 0}, counts{1, 11214, 3};
h5xx::slice slice(offsets, counts);
h5xx::read_dataset(ds, arr, slice);
return arr;
}
int main()
{
print_array(read_frame(9));
}
first of all, forgive my code for being ugly. The tons of ideas I've been given to try to fix this code have jumbled it up after all the potential solutions that haven't worked. Basically, I'm coding a Hearthstone rip-off that reads in two .txt files with card information and battles them to see which player wins. The issue is that when I'm trying to save the player's name (the first line in the files), it saves the whole file instead of just the first line. When I have managed to fix that, the for loop used to save the information for the card objects (format: card name, card power, card health) does not get saved properly for some reason. Any help would be appreciated, I've been trying to fix this for two days and nothing has fully solved the problem. I'll attach the read in files first before the code.
Disclaimer: It's a lot of lines and I'm sorry about that. Also I think the problem could be that my Mac is not saving the .txt in a format that has the right line endings. I'm using XCode as my IDE. Thank you so much to whomever is willing to help!
File1:
The Innkeeper
3
Tunnel Trogg
1
3
Neptulon
7
7
Fire Elemental
6
5
File2:
Malfurion
3
Leper Gnome
2
1
Aviana
5
5
Cenarius
5
8
Main:
#include "Player.h"
using namespace std;
int main()
{
cout << "Please enter file name of the first player: " << endl;
string inFile = "";
getline(cin, inFile);
Player* p1 = new Player(inFile);
cout << "Now enter the file name of the second player: " << endl;
getline(cin, inFile);
Player* p2 = new Player(inFile);
p1->battle(*p2);
delete p1;
delete p2;
return 0;
}
Player Header:
#include "Card.h"
#include <fstream>
#ifndef Player_h
#define Player_h
using namespace std;
class Player
{
private:
string playerName;
int numCards;
Card ** cards;
int wins = 0;
public:
Player(std::string inFile);
void battle(Player p2);
Card* getCard(int counter);
~Player();
};
#endif /* Player_h */
Card Header:
#include <string>
#include <iostream>
#ifndef Card_h
#define Card_h
using namespace std;
class Card
{
public:
Card();
string getName();
int getPower();
int getHealth();
void setName(string newName);
void setPower(int newPower);
void setHealth(int newHealth);
Card* duel(Card&);
friend ostream& operator<<(ostream& o, Card& c);
friend bool operator==(Card& p1Card, Card& p2Card);
private:
string name;
int power;
int health;
};
#endif /* Card_h */
Player Source:
#include "Player.h"
using namespace std;
Player::Player(string inFile)
{
ifstream in(inFile, ios::in);\
if (!in)
{
cerr << "There was a problem opening the file. Sorry, try again!" << endl;
return;
}
getline(in, playerName);
cout << playerName << endl;
in>>numCards;
playerName = "";
numCards = 0;
cards = new Card* [numCards];
string tempName = "";
int tempPower = 0;
int tempHealth = 0;
for (int i = 0; i<numCards; i++)
{
in.ignore();
cards[i] = new Card();
getline(in, tempName);
cout << "in for loop: " << endl;
cout << tempName << ",";
cards[i]->setName(tempName);
in >> tempPower;
in.ignore();
cout << tempPower << ",";
cards[i]->setPower(tempPower);
in >> tempHealth;
cout << tempHealth << " done"<< endl;
cards[i]->setHealth(tempHealth);
}
}
void Player::battle(Player p2)
{
int draws = 0;
cout << "Let the battle begin!" << endl;
cout << numCards << endl;
if (wins > p2.wins)
{
cout << playerName << " wins over " << p2.playerName << ", " << wins << " to " << p2.wins;
if (draws == 0)
{
cout << " and no ties." << endl;
}
else
{
cout << " and " << draws << " ties." << endl;
}
}
else if (p2.wins > wins)
{
cout << p2.playerName << " wins over " << playerName << ", " << p2.wins << " to " << wins;
if (draws == 0)
{
cout << " and no ties." << endl;
}
else
{
cout << " and " << draws << " ties." << endl;
}
}
else if (p2.wins == wins)
{
cout << "It is a draw between " << playerName << " and " << p2.playerName << ", with " << wins << " for each and ";
if (draws == 0)
{
cout << "no ties." << endl;
}
else
{
cout << draws << " ties." << endl;
}
}
cout << "Here are the detailed results:" << endl;
for (int i = 0; i < numCards; i++)
{
cout << *cards[i] << " vs. " << *p2.cards[i] << " - ";
if (*cards[i] == *p2.cards[i])
{
cout << "It is a draw." << endl;
}
else if (cards[i]->duel(*p2.cards[i]) == NULL)
{
cout << "It is a draw." << endl;
}
else if (*cards[i]->duel(*p2.cards[i]) == *p2.cards[i])
{
cout << p2.cards[i]->getName() << "wins for " << p2.playerName << "." << endl;
}
else if (*cards[i]->duel(*p2.cards[i]) == *cards[i])
{
cout << cards[i]->getName() << "wins for " << playerName << "." << endl;
}
}
}
Player::~Player()
{
if (cards != NULL)
{
for (int i = 0; i < numCards; i++)
{
if (cards[i] != nullptr)
{
delete cards[i];
cards[i] = NULL;
}
};
}
}
Card Source:
#include "Card.h"
using namespace std;
Card::Card()
{
name = "";
power = 0;
health = 0;
}
string Card::getName()
{
return name;
}
int Card::getPower()
{
return power;
}
int Card::getHealth()
{
return health;
}
void Card::setName(string newName)
{
name = newName;
}
void Card::setPower(int newPower)
{
power = newPower;
}
void Card::setHealth(int newHealth)
{
health = newHealth;
}
Card* Card::duel(Card& otherCard)
{
if ((otherCard.getHealth() - this->getPower() <=0) && (getHealth() - otherCard.getPower() <= 0))
{
return NULL;
}
else if ((otherCard.getHealth() - this->getPower() >0) && (getHealth() - otherCard.getPower() >0))
{
return NULL;
}
else if (otherCard.getHealth() - this->getPower() <=0)
{
return this;
}
else if (this->getHealth() - otherCard.getPower() <=0)
{
return &otherCard;
}
return NULL;
}
ostream& operator<<(ostream& o, Card& c)
{
o << c.getName() << " (" << c.power << ", " << c.health << ") " << endl;
return o;
}
bool operator==(Card& p1Card, Card& p2Card)
{
if (p1Card.health == p2Card.health &&
p1Card.power == p2Card.power &&
p1Card.name == p2Card.name)
{
return true;
}
else
{
return false;
}
}
Your code is almost right. It can read the Player's name and the card numbers, but your codes showed below:
in>>numCards;
playerName = "";
numCards = 0;
cards = new Card* [numCards];
at first, it read the num of card and store it to numCards, it is right.
next, you clear the value of the numCards, then, you lost the num of the Card, so the codes followed it are executed with numCards == 0
You can just comment the line numCards = 0, and your code is executed right.