1. CoGAPS
  2. src
  3. file_parser
  4. MtxParser.cpp
Browse code

Correct the parsing in mtx files

This patch makes sure that MatrixElement is handling all of the
string parsing in the input data files. Previously, MtxParser was
doing this separetly and passing a float value. This by-passed the
error checking in MatrixElement and caused some errors to be
missed.

Tom Sherman authored on 22/07/2019 20:46:20
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @2ac581010
... ... 
@@ -54,7 +54,7 @@ MatrixElement MtxParser::getNext()
54 54 
 {
55 55 
     unsigned row = 0;
56 56 
     unsigned col = 0;
57 
-    float val = 0.f;
57 
+    std::string val;
58 58 
     mFile >> row;
59 59 
     mFile >> col;
60 60 
     mFile >> val;
Browse code

clean up mtx parser

sherman5 authored on 20/06/2019 20:51:32
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @f84bfc807
... ... 
@@ -9,28 +9,41 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
9 9 
 {
10 10 
     mFile.open(path.c_str());
11 11
12 
-    std::string line;
13 
-    std::getline(mFile, line);
14 
-    if (mFile.eof() || mFile.fail())
15 
-    {
16 
-        GAPS_ERROR("Invalid MTX file");
17 
-    }
18 
-
19 12 
     // skip over comments
13 
+    std::string line = "%";
20 14 
     while (line.find('%') != std::string::npos)
21 15 
     {
22 16 
         std::getline(mFile, line);
23 
-        if (mFile.eof() || mFile.fail())
24 
-        {
25 
-            GAPS_ERROR("Invalid MTX file");
26 
-        }
17 
+        checkFileState();
27 18 
     }
28 
-    std::stringstream ss(line); // this line contains dimensions
29 19
30 
-    // store dimensions
20 
+    std::stringstream ss(line); // this line contains dimensions
31 21 
     ss >> mNumRows >> mNumCols;
32 22 
 }
33 23
24 
+MtxParser::~MtxParser()
25 
+{
26 
+    mFile.close();
27 
+}
28 
+
29 
+unsigned MtxParser::nRow() const
30 
+{
31 
+    return mNumRows;
32 
+}
33 
+
34 
+unsigned MtxParser::nCol() const
35 
+{
36 
+    return mNumCols;
37 
+}
38 
+
39 
+void MtxParser::checkFileState() const
40 
+{
41 
+    if (mFile.eof() || mFile.fail())
42 
+    {
43 
+        GAPS_ERROR("Invalid MTX file");
44 
+    }
45 
+}
46 
+
34 47 
 bool MtxParser::hasNext()
35 48 
 {
36 49 
     mFile >> std::ws; // get rid of whitespace
... ... 
@@ -39,7 +52,8 @@ bool MtxParser::hasNext()
39 52
40 53 
 MatrixElement MtxParser::getNext()
41 54 
 {
42 
-    unsigned row = 0, col = 0;
55 
+    unsigned row = 0;
56 
+    unsigned col = 0;
43 57 
     float val = 0.f;
44 58 
     mFile >> row;
45 59 
     mFile >> col;
Browse code

added blank Hdf5Parser class

Tom Sherman authored on 09/01/2019 18:25:20
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @4daa5452c
... ... 
@@ -3,23 +3,10 @@
3 3
4 4 
 #include "../utils/GapsAssert.h"
5 5
6 
-//#include <cstdio>
7 
-//#include <cunistd>
8 6 
 #include <sstream>
9 7
10 8 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
11 9 
 {
12 
-    // check if file exists and read it in
13 
-    //if (access(path, F_OK) == -1)
14 
-    //{
15 
-    //    GAPS_ERROR("Invalid MTX file");
16 
-    //}
17 
-    //mFile = fopen(path, "r");
18 
-
19 
-    // read first line
20 
-    //char line[1024];
21 
-    //fgets(line, 1024, mFile);
22 
-
23 10 
     mFile.open(path.c_str());
24 11
25 12 
     std::string line;
... ... 
@@ -42,7 +29,6 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
42 29
43 30 
     // store dimensions
44 31 
     ss >> mNumRows >> mNumCols;
45 
-    //mFile_p = fopen(path, "r");
46 32 
 }
47 33
48 34 
 bool MtxParser::hasNext()
... ... 
@@ -55,10 +41,8 @@ MatrixElement MtxParser::getNext()
55 41 
 {
56 42 
     unsigned row = 0, col = 0;
57 43 
     float val = 0.f;
58 
-
59 44 
     mFile >> row;
60 45 
     mFile >> col;
61 46 
     mFile >> val;
62 
-
63 47 
     return MatrixElement(row - 1, col - 1, val);
64 48 
 }
Browse code

implemented policy based design for sparse/dense storage in the GibbsSampler

Tom Sherman authored on 08/01/2019 22:16:52
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @c8c9b6059
... ... 
@@ -3,26 +3,31 @@
3 3
4 4 
 #include "../utils/GapsAssert.h"
5 5
6 
-#include <cstdio>
7 
-#include <cunistd>
6 
+//#include <cstdio>
7 
+//#include <cunistd>
8 8 
 #include <sstream>
9 9
10 10 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
11 11 
 {
12 12 
     // check if file exists and read it in
13 
-    if (access(path, F_OK) == -1)
14 
-    {
15 
-        GAPS_ERROR("Invalid MTX file");
16 
-    }
17 
-    mFile = fopen(path, "r");
13 
+    //if (access(path, F_OK) == -1)
14 
+    //{
15 
+    //    GAPS_ERROR("Invalid MTX file");
16 
+    //}
17 
+    //mFile = fopen(path, "r");
18 18
19 19 
     // read first line
20 
-    char line[1024];
21 
-    fgets(line, 1024, mFile);
20 
+    //char line[1024];
21 
+    //fgets(line, 1024, mFile);
22 22
23 
+    mFile.open(path.c_str());
23 24
24 25 
     std::string line;
25 26 
     std::getline(mFile, line);
27 
+    if (mFile.eof() || mFile.fail())
28 
+    {
29 
+        GAPS_ERROR("Invalid MTX file");
30 
+    }
26 31
27 32 
     // skip over comments
28 33 
     while (line.find('%') != std::string::npos)
... ... 
@@ -37,7 +42,7 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
37 42
38 43 
     // store dimensions
39 44 
     ss >> mNumRows >> mNumCols;
40 
-    mFile_p = fopen(path, "r");
45 
+    //mFile_p = fopen(path, "r");
41 46 
 }
42 47
43 48 
 bool MtxParser::hasNext()
... ... 
@@ -51,13 +56,9 @@ MatrixElement MtxParser::getNext()
51 56 
     unsigned row = 0, col = 0;
52 57 
     float val = 0.f;
53 58
54 
-
55 
-
56 
-    //mFile >> row;
57 
-    //mFile >> col;
58 
-    //mFile >> val;
59 
-
60 
-
59 
+    mFile >> row;
60 
+    mFile >> col;
61 
+    mFile >> val;
61 62
62 63 
     return MatrixElement(row - 1, col - 1, val);
63 64 
 }
Browse code

link against Rhdf5 library

Tom Sherman authored on 08/01/2019 15:10:46
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @3711db62c
... ... 
@@ -3,19 +3,26 @@
3 3
4 4 
 #include "../utils/GapsAssert.h"
5 5
6 
+#include <cstdio>
7 
+#include <cunistd>
6 8 
 #include <sstream>
7 9
8 10 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
9 11 
 {
10 
-    mFile.open(path.c_str());
12 
+    // check if file exists and read it in
13 
+    if (access(path, F_OK) == -1)
14 
+    {
15 
+        GAPS_ERROR("Invalid MTX file");
16 
+    }
17 
+    mFile = fopen(path, "r");
11 18
12 19 
     // read first line
20 
+    char line[1024];
21 
+    fgets(line, 1024, mFile);
22 
+
23 
+
13 24 
     std::string line;
14 25 
     std::getline(mFile, line);
15 
-    if (mFile.eof() || mFile.fail())
16 
-    {
17 
-        GAPS_ERROR("Invalid MTX file");
18 
-    }
19 26
20 27 
     // skip over comments
21 28 
     while (line.find('%') != std::string::npos)
... ... 
@@ -30,6 +37,7 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
30 37
31 38 
     // store dimensions
32 39 
     ss >> mNumRows >> mNumCols;
40 
+    mFile_p = fopen(path, "r");
33 41 
 }
34 42
35 43 
 bool MtxParser::hasNext()
... ... 
@@ -43,9 +51,13 @@ MatrixElement MtxParser::getNext()
43 51 
     unsigned row = 0, col = 0;
44 52 
     float val = 0.f;
45 53
46 
-    mFile >> row;
47 
-    mFile >> col;
48 
-    mFile >> val;
54 
+
55 
+
56 
+    //mFile >> row;
57 
+    //mFile >> col;
58 
+    //mFile >> val;
59 
+
60 
+
49 61
50 62 
     return MatrixElement(row - 1, col - 1, val);
51 63 
 }
Browse code

updated config to commit file permissions

Tom Sherman authored on 29/10/2018 19:56:14
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @9cde329dd
1 1 
old mode 100644
2 2 
new mode 100755
Browse code

started making changes

Tom Sherman authored on 28/08/2018 19:53:08
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @8f9d41615
... ... 
@@ -1,7 +1,7 @@
1 1 
 #include "MatrixElement.h"
2 2 
 #include "MtxParser.h"
3 3
4 
-#include "../GapsAssert.h"
4 
+#include "../utils/GapsAssert.h"
5 5
6 6 
 #include <sstream>
7 7
Browse code

merge

Tom Sherman authored on 18/06/2018 21:11:30
Showing0 changed files
Browse code

make sure includes are correct for CLI

Tom Sherman authored on 18/06/2018 17:07:27
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @b38a2da2b
... ... 
@@ -3,7 +3,6 @@
3 3 
 #include "../GapsAssert.h"
4 4
5 5 
 #include <sstream>
6 
-#include <Rcpp.h>
7 6
8 7 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
9 8 
 {
Browse code

added back PUMP and FixedPatterns option

Tom Sherman authored on 13/06/2018 21:35:14
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @dd3a94412
... ... 
@@ -1,10 +1,12 @@
1 
-#include "MtxParser.h"
2 1 
 #include "MatrixElement.h"
2 
+#include "MtxParser.h"
3 
+
3 4 
 #include "../GapsAssert.h"
4 5
5 
-#include <sstream>
6 6 
 #include <Rcpp.h>
7 7
8 
+#include <sstream>
9 
+
8 10 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
9 11 
 {
10 12 
     mFile.open(path.c_str());
Browse code

passing package checks

Tom Sherman authored on 12/06/2018 19:23:36
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @7de32bf9e
... ... 
@@ -1,17 +1,30 @@
1 1 
 #include "MtxParser.h"
2 2 
 #include "MatrixElement.h"
3 
+#include "../GapsAssert.h"
3 4
4 5 
 #include <sstream>
6 
+#include <Rcpp.h>
5 7
6 8 
 MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
7 9 
 {
8 10 
     mFile.open(path.c_str());
9 11
12 
+    // read first line
13 
+    std::string line;
14 
+    std::getline(mFile, line);
15 
+    if (mFile.eof() || mFile.fail())
16 
+    {
17 
+        GAPS_ERROR("Invalid MTX file");
18 
+    }
19 
+
10 20 
     // skip over comments
11 
-    std::string line = "%";
12 21 
     while (line.find('%') != std::string::npos)
13 22 
     {
14 23 
         std::getline(mFile, line);
24 
+        if (mFile.eof() || mFile.fail())
25 
+        {
26 
+            GAPS_ERROR("Invalid MTX file");
27 
+        }
15 28 
     }
16 29 
     std::stringstream ss(line); // this line contains dimensions
17 30
... ... 
@@ -21,17 +34,18 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
21 34
22 35 
 bool MtxParser::hasNext()
23 36 
 {
37 
+    mFile >> std::ws; // get rid of whitespace
24 38 
     return mFile.peek() != EOF;
25 39 
 }
26 40
27 41 
 MatrixElement MtxParser::getNext()
28 42 
 {
29 
-    MatrixElement e(0, 0, 0.f);
30 
-    unsigned buff;
31 
-    mFile >> buff;
32 
-    e.dim[0] = buff - 1;
33 
-    mFile >> buff;
34 
-    e.dim[1] = buff - 1;
35 
-    mFile >> e.value;
36 
-    return e;
43 
+    unsigned row = 0, col = 0;
44 
+    float val = 0.f;
45 
+
46 
+    mFile >> row;
47 
+    mFile >> col;
48 
+    mFile >> val;
49 
+
50 
+    return MatrixElement(row - 1, col - 1, val);
37 51 
 }
Browse code

Fixed MtxParser and added file parser unit tests as well as read matrix from mtx file unit tests

Tiger Gao authored on 11/06/2018 20:45:57
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @fa403571a
... ... 
@@ -27,6 +27,11 @@ bool MtxParser::hasNext()
27 27 
 MatrixElement MtxParser::getNext()
28 28 
 {
29 29 
     MatrixElement e(0, 0, 0.f);
30 
-    mFile >> e.dim[0] >> e.dim[1] >> e.value;
30 
+    unsigned buff;
31 
+    mFile >> buff;
32 
+    e.dim[0] = buff - 1;
33 
+    mFile >> buff;
34 
+    e.dim[1] = buff - 1;
35 
+    mFile >> e.value;
31 36 
     return e;
32 37 
 }
Browse code

Optimized matrix constructor and improved readibility

Tiger Gao authored on 08/06/2018 16:59:24
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @17bd0769a
... ... 
@@ -14,7 +14,7 @@ MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
14 14 
         std::getline(mFile, line);
15 15 
     }
16 16 
     std::stringstream ss(line); // this line contains dimensions
17 
-
17 
+
18 18 
     // store dimensions
19 19 
     ss >> mNumRows >> mNumCols;
20 20 
 }
... ... 
@@ -27,6 +27,6 @@ bool MtxParser::hasNext()
27 27 
 MatrixElement MtxParser::getNext()
28 28 
 {
29 29 
     MatrixElement e(0, 0, 0.f);
30 
-    mFile >> e.row >> e.col >> e.value;
30 
+    mFile >> e.dim[0] >> e.dim[1] >> e.value;
31 31 
     return e;
32 32 
 }
Browse code

make lintr happy

Tom Sherman authored on 31/05/2018 21:28:52
Showing1 changed files
src/file_parser/MtxParser.cpp
History View file @743777199
1 1 
new file mode 100644
... ... 
@@ -0,0 +1,32 @@
1 
+#include "MtxParser.h"
2 
+#include "MatrixElement.h"
3 
+
4 
+#include <sstream>
5 
+
6 
+MtxParser::MtxParser(const std::string &path) : mNumRows(0), mNumCols(0)
7 
+{
8 
+    mFile.open(path.c_str());
9 
+
10 
+    // skip over comments
11 
+    std::string line = "%";
12 
+    while (line.find('%') != std::string::npos)
13 
+    {
14 
+        std::getline(mFile, line);
15 
+    }
16 
+    std::stringstream ss(line); // this line contains dimensions
17 
+
18 
+    // store dimensions
19 
+    ss >> mNumRows >> mNumCols;
20 
+}
21 
+
22 
+bool MtxParser::hasNext()
23 
+{
24 
+    return mFile.peek() != EOF;
25 
+}
26 
+
27 
+MatrixElement MtxParser::getNext()
28 
+{
29 
+    MatrixElement e(0, 0, 0.f);
30 
+    mFile >> e.row >> e.col >> e.value;
31 
+    return e;
32 
+}