tifffile 0.0.1 → 0.0.2
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- checksums.yaml +4 -4
- data/.gemspec +2 -2
- data/Rakefile +8 -0
- data/analyzer.py +28 -0
- data/ext/tifffile/extconf.rb +7 -2
- data/ext/tifffile/tifffile.cpp +237 -0
- data/lib/tifffile.rb +26 -0
- data/lib/tifffile/version.rb +2 -2
- data/spec/tifffile_spec.rb +7 -0
- metadata +5 -4
- data/ext/tifffile/tifffile.c +0 -74
- data/ext/tifffile/tifffile.h +0 -1
checksums.yaml
CHANGED
@@ -1,7 +1,7 @@
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---
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SHA1:
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-
metadata.gz:
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data.tar.gz:
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metadata.gz: 73ee12cfcfb7b19f45966c553780006c9e2ea981
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data.tar.gz: aadabb05a8725757870334ebdffec87f22d0451d
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5
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SHA512:
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6
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-
metadata.gz:
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7
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-
data.tar.gz:
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6
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+
metadata.gz: 7713c2989ad9be58d24c32cdb9dc63ea10971f32c376102627e442efe013b0e7d5492118ace195b65af387c0538a3e77b96d93f1d23a06f955880712d57a590a
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7
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+
data.tar.gz: 072ec891538ef01d00efd6210417ad0d90e7cf6b877f716cf72a8caab050841f14bfc9c50d4c37d9dee9373d60d8da2bab112f53c187e30aa64d1a2f55f23612
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data/.gemspec
CHANGED
@@ -2,8 +2,8 @@ require File.expand_path("../lib/tifffile/version", __FILE__)
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2
2
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3
3
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Gem::Specification.new do |gem|
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4
4
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gem.name = 'tifffile'
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5
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-
gem.version =
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6
|
-
gem.date = '2016-03-
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5
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+
gem.version = TiffFileVersion::VERSION
|
6
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+
gem.date = '2016-03-22'
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7
7
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8
8
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gem.summary = "TIFF reader and writer"
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9
9
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gem.description = ""
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data/Rakefile
CHANGED
@@ -1,6 +1,14 @@
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1
1
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require "rake/extensiontask"
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2
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+
require 'rspec/core'
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3
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+
require 'rspec/core/rake_task'
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4
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+
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2
5
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|
3
6
|
Rake::ExtensionTask.new "tifffile" do |ext|
|
4
7
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ext.lib_dir = "lib/tifffile"
|
5
8
|
end
|
6
9
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|
10
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+
RSpec::Core::RakeTask.new(:spec) do |spec|
|
11
|
+
Rake::Task['compile'].invoke
|
12
|
+
spec.pattern = FileList['spec/**/*_spec.rb']
|
13
|
+
end
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14
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+
|
data/analyzer.py
ADDED
@@ -0,0 +1,28 @@
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1
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+
#!/usr/bin/python
|
2
|
+
|
3
|
+
import numpy as np
|
4
|
+
from libtiff import TIFFfile
|
5
|
+
from libtiff import TIFF
|
6
|
+
|
7
|
+
def read(fileName):
|
8
|
+
"""
|
9
|
+
Script to import tif file from imageJ,
|
10
|
+
usage: zstack = tiff.read(inFileName)
|
11
|
+
PTW 2015/01/29
|
12
|
+
"""
|
13
|
+
tiff = TIFFfile(fileName)
|
14
|
+
samples, sample_names = tiff.get_samples()
|
15
|
+
|
16
|
+
outList = []
|
17
|
+
for sample in samples:
|
18
|
+
outList.append(np.copy(sample)[...,np.newaxis])
|
19
|
+
|
20
|
+
out = np.concatenate(outList,axis=-1)
|
21
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+
out = np.rollaxis(out,0,3)
|
22
|
+
out = np.flipud(out)
|
23
|
+
|
24
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+
tiff.close()
|
25
|
+
|
26
|
+
return out
|
27
|
+
|
28
|
+
print(read('a.tiff'))
|
data/ext/tifffile/extconf.rb
CHANGED
@@ -0,0 +1,237 @@
|
|
1
|
+
#include <ruby.h>
|
2
|
+
#include <stdio.h>
|
3
|
+
#include <stdlib.h>
|
4
|
+
#include <string>
|
5
|
+
#include "tiffio.h"
|
6
|
+
#include <vector>
|
7
|
+
#include <algorithm>
|
8
|
+
|
9
|
+
using namespace std;
|
10
|
+
|
11
|
+
template <class T>
|
12
|
+
static bool rows_size_compare(std::vector<T> & a, std::vector<T> & b)
|
13
|
+
{
|
14
|
+
return (a.size() < b.size());
|
15
|
+
}
|
16
|
+
|
17
|
+
template <class T>
|
18
|
+
void calculate_width_height(std::vector<std::vector<T> > & data, uint32 & width, uint32 & height){
|
19
|
+
height = data.size();
|
20
|
+
width = std::max_element(data.begin(), data.end(), rows_size_compare<T>)->size();
|
21
|
+
}
|
22
|
+
|
23
|
+
|
24
|
+
template <class T>
|
25
|
+
void write_data_to_row_buffer(std::vector<T> & data, unsigned char *buf, uint64 buff_size, uint8 sampleperpixel, uint8 bitspersample){
|
26
|
+
memset(buf, 0, buff_size);
|
27
|
+
buff_size = std::min<uint64>(buff_size, sizeof(T) * data.size());
|
28
|
+
memcpy(buf, (void *)(&(data[0])), buff_size);
|
29
|
+
}
|
30
|
+
|
31
|
+
|
32
|
+
template <class T>
|
33
|
+
bool write_tiff_file(std::string filename, std::vector<std::vector<T> > & data, uint8 sampleperpixel, uint8 bitspersample, std::string description, std::string software){
|
34
|
+
try {
|
35
|
+
TIFF* tif = TIFFOpen(filename.c_str(), "w");
|
36
|
+
|
37
|
+
uint32 width, height;
|
38
|
+
calculate_width_height(data, width, height);
|
39
|
+
|
40
|
+
TIFFSetField(tif, TIFFTAG_IMAGEWIDTH, width);
|
41
|
+
TIFFSetField(tif, TIFFTAG_IMAGELENGTH, height);
|
42
|
+
TIFFSetField(tif, TIFFTAG_SAMPLESPERPIXEL, sampleperpixel);
|
43
|
+
TIFFSetField(tif, TIFFTAG_BITSPERSAMPLE, bitspersample);
|
44
|
+
TIFFSetField(tif, TIFFTAG_ORIENTATION, (int)ORIENTATION_TOPLEFT);
|
45
|
+
TIFFSetField(tif, TIFFTAG_PLANARCONFIG, PLANARCONFIG_CONTIG);
|
46
|
+
TIFFSetField(tif, TIFFTAG_COMPRESSION, COMPRESSION_NONE);
|
47
|
+
TIFFSetField(tif, TIFFTAG_PHOTOMETRIC, PHOTOMETRIC_MINISBLACK);
|
48
|
+
TIFFSetField(tif, TIFFTAG_IMAGEDESCRIPTION, (char*)description.c_str());
|
49
|
+
TIFFSetField(tif, TIFFTAG_SOFTWARE, (char*)software.c_str());
|
50
|
+
|
51
|
+
uint64 linebytes = sampleperpixel * width * (bitspersample / 8);
|
52
|
+
unsigned char *buf = NULL;
|
53
|
+
buf = (unsigned char *)_TIFFmalloc(linebytes);
|
54
|
+
|
55
|
+
TIFFSetField(tif, TIFFTAG_ROWSPERSTRIP, 1);
|
56
|
+
|
57
|
+
for (uint32 row = 0; row < height; row++){
|
58
|
+
std::vector<T> row_data = data[row];
|
59
|
+
write_data_to_row_buffer(row_data, buf, linebytes, sampleperpixel, bitspersample);
|
60
|
+
if (TIFFWriteScanline(tif, buf, row, 0) < 0)
|
61
|
+
break;
|
62
|
+
}
|
63
|
+
|
64
|
+
if (buf)
|
65
|
+
_TIFFfree(buf);
|
66
|
+
|
67
|
+
TIFFClose(tif);
|
68
|
+
}
|
69
|
+
catch (...){
|
70
|
+
return false;
|
71
|
+
}
|
72
|
+
return true;
|
73
|
+
}
|
74
|
+
|
75
|
+
|
76
|
+
bool get_matrix_element_type(VALUE data_matrix, bool &is_float){
|
77
|
+
if (!RB_TYPE_P(data_matrix, T_ARRAY) || RARRAY_LEN(data_matrix) < 1)
|
78
|
+
return false;
|
79
|
+
|
80
|
+
VALUE first_row = RARRAY_PTR(data_matrix)[0];
|
81
|
+
|
82
|
+
if (!RB_TYPE_P(first_row, T_ARRAY) || RARRAY_LEN(first_row) < 1)
|
83
|
+
return false;
|
84
|
+
|
85
|
+
VALUE first_item = RARRAY_PTR(first_row)[0];
|
86
|
+
|
87
|
+
if (!RB_TYPE_P(first_item, T_FIXNUM) && !RB_TYPE_P(first_item, T_FLOAT))
|
88
|
+
return false;
|
89
|
+
|
90
|
+
is_float = RB_TYPE_P(first_item, T_FLOAT);
|
91
|
+
|
92
|
+
return true;
|
93
|
+
}
|
94
|
+
|
95
|
+
template <class F, class T>
|
96
|
+
vector<vector<T> > matrix_type_cast(vector<vector<F> > & from){
|
97
|
+
vector<vector<T> > result;
|
98
|
+
result.resize(from.size());
|
99
|
+
|
100
|
+
for (int i = 0; i < from.size(); i++)
|
101
|
+
result[i].assign(from[i].begin(), from[i].end());
|
102
|
+
|
103
|
+
return result;
|
104
|
+
};
|
105
|
+
|
106
|
+
VALUE TiffFile = Qnil;
|
107
|
+
|
108
|
+
VALUE method_tifffile_converter_to_tiff(VALUE self, VALUE filename, VALUE data_matrix, VALUE sample_size, VALUE sample_unsigned, VALUE description, VALUE software){
|
109
|
+
data_matrix = rb_check_array_type(data_matrix);
|
110
|
+
|
111
|
+
|
112
|
+
Check_Type(filename, T_STRING);
|
113
|
+
Check_Type(data_matrix, T_ARRAY);
|
114
|
+
Check_Type(sample_size, T_FIXNUM);
|
115
|
+
Check_Type(description, T_STRING);
|
116
|
+
Check_Type(software, T_STRING);
|
117
|
+
|
118
|
+
uint8 size = std::min<uint8>(NUM2USHORT(sample_size), 8);
|
119
|
+
|
120
|
+
bool unsigned_flag = RTEST(sample_unsigned);
|
121
|
+
|
122
|
+
bool is_float_matrix;
|
123
|
+
if (!get_matrix_element_type(data_matrix, is_float_matrix))
|
124
|
+
rb_raise(rb_eRuntimeError, "Invalid matrix items type");
|
125
|
+
|
126
|
+
if (size != 1 && size != 2 && size != 4 && size != 8)
|
127
|
+
rb_raise(rb_eRuntimeError, "Sample size should be in range [1, 2, 4, 8]");
|
128
|
+
|
129
|
+
if (is_float_matrix && (size % 4) != 0)
|
130
|
+
rb_raise(rb_eRuntimeError, "Sample size should be 4 or 8 on non-fixnum matrix");
|
131
|
+
|
132
|
+
vector<vector<double> > data_d;
|
133
|
+
vector<double> temp_d;
|
134
|
+
vector<vector<int64> > data_i;
|
135
|
+
vector<int64> temp_i;
|
136
|
+
|
137
|
+
VALUE row, item;
|
138
|
+
|
139
|
+
if (is_float_matrix)
|
140
|
+
data_d.resize(RARRAY_LEN(data_matrix));
|
141
|
+
else
|
142
|
+
data_i.resize(RARRAY_LEN(data_matrix));
|
143
|
+
|
144
|
+
|
145
|
+
for (long i = 0; i < RARRAY_LEN(data_matrix); i++){
|
146
|
+
row = RARRAY_PTR(data_matrix)[i];
|
147
|
+
|
148
|
+
if (!RB_TYPE_P(row, T_ARRAY))
|
149
|
+
rb_raise(rb_eRuntimeError, "Matrix row %ld is not an array", i);
|
150
|
+
|
151
|
+
// Clear row buffer
|
152
|
+
if (is_float_matrix){
|
153
|
+
temp_d.clear();
|
154
|
+
temp_d.resize(RARRAY_LEN(row));
|
155
|
+
} else {
|
156
|
+
temp_i.clear();
|
157
|
+
temp_i.resize(RARRAY_LEN(row));
|
158
|
+
}
|
159
|
+
|
160
|
+
|
161
|
+
// Read row
|
162
|
+
for (long j = 0; j < RARRAY_LEN(row); j++){
|
163
|
+
item = RARRAY_PTR(row)[j];
|
164
|
+
Check_Type(item, is_float_matrix ? T_FLOAT : T_FIXNUM);
|
165
|
+
if (is_float_matrix)
|
166
|
+
temp_d[j] = RFLOAT_VALUE(item);
|
167
|
+
else
|
168
|
+
temp_i[j] = FIX2LONG(item);
|
169
|
+
}
|
170
|
+
|
171
|
+
if (is_float_matrix)
|
172
|
+
data_d[i] = temp_d;
|
173
|
+
else
|
174
|
+
data_i[i] = temp_i;
|
175
|
+
}
|
176
|
+
|
177
|
+
|
178
|
+
bool result = false;
|
179
|
+
if (is_float_matrix){
|
180
|
+
if (size == 8)
|
181
|
+
result = write_tiff_file<double>(StringValuePtr(filename), data_d, 1, 64, StringValuePtr(description), StringValuePtr(software));
|
182
|
+
else if (size == 4){
|
183
|
+
vector<vector<float> > cast_buffer = matrix_type_cast<double, float>(data_d);
|
184
|
+
result = write_tiff_file<float>(StringValuePtr(filename), cast_buffer, 1, 32, StringValuePtr(description), StringValuePtr(software));
|
185
|
+
}
|
186
|
+
else
|
187
|
+
rb_raise(rb_eRuntimeError, "unrecognized sample size for float matrix : %d", size);
|
188
|
+
}
|
189
|
+
else {
|
190
|
+
if (unsigned_flag){
|
191
|
+
if (size == 8){
|
192
|
+
vector<vector<uint64> > cast_buffer = matrix_type_cast<int64, uint64>(data_i);
|
193
|
+
result = write_tiff_file<uint64>(StringValuePtr(filename), cast_buffer, 1, 64, StringValuePtr(description), StringValuePtr(software));
|
194
|
+
}
|
195
|
+
else if (size == 4){
|
196
|
+
vector<vector<uint32> > cast_buffer = matrix_type_cast<int64, uint32>(data_i);
|
197
|
+
result = write_tiff_file<uint32>(StringValuePtr(filename), cast_buffer, 1, 32, StringValuePtr(description), StringValuePtr(software));
|
198
|
+
}
|
199
|
+
else if (size == 2){
|
200
|
+
vector<vector<uint16> > cast_buffer = matrix_type_cast<int64, uint16>(data_i);
|
201
|
+
result = write_tiff_file<uint16>(StringValuePtr(filename), cast_buffer, 1, 16, StringValuePtr(description), StringValuePtr(software));
|
202
|
+
}
|
203
|
+
else if (size == 1){
|
204
|
+
vector<vector<uint8> > cast_buffer = matrix_type_cast<int64, uint8>(data_i);
|
205
|
+
result = write_tiff_file<uint8>(StringValuePtr(filename), cast_buffer, 1, 8, StringValuePtr(description), StringValuePtr(software));
|
206
|
+
}
|
207
|
+
else
|
208
|
+
rb_raise(rb_eRuntimeError, "unrecognized sample size for unsigned numeric matrix : %d", size);
|
209
|
+
}
|
210
|
+
else {
|
211
|
+
if (size == 8){
|
212
|
+
result = write_tiff_file<int64>(StringValuePtr(filename), data_i, 1, 64, StringValuePtr(description), StringValuePtr(software));
|
213
|
+
}
|
214
|
+
else if (size == 4){
|
215
|
+
vector<vector<int32> > cast_buffer = matrix_type_cast<int64, int32>(data_i);
|
216
|
+
result = write_tiff_file<int32>(StringValuePtr(filename), cast_buffer, 1, 32, StringValuePtr(description), StringValuePtr(software));
|
217
|
+
}
|
218
|
+
else if (size == 2){
|
219
|
+
vector<vector<int16> > cast_buffer = matrix_type_cast<int64, int16>(data_i);
|
220
|
+
result = write_tiff_file<int16>(StringValuePtr(filename), cast_buffer, 1, 16, StringValuePtr(description), StringValuePtr(software));
|
221
|
+
}
|
222
|
+
else if (size == 1){
|
223
|
+
vector<vector<int8> > cast_buffer = matrix_type_cast<int64, int8>(data_i);
|
224
|
+
result = write_tiff_file<int8>(StringValuePtr(filename), cast_buffer, 1, 8, StringValuePtr(description), StringValuePtr(software));
|
225
|
+
}
|
226
|
+
else
|
227
|
+
rb_raise(rb_eRuntimeError, "unrecognized sample size for signed numeric matrix : %d", size);
|
228
|
+
}
|
229
|
+
}
|
230
|
+
|
231
|
+
return result ? Qtrue : Qfalse;
|
232
|
+
}
|
233
|
+
|
234
|
+
extern "C" void Init_tifffile(){
|
235
|
+
TiffFile = rb_define_module("TiffFile");
|
236
|
+
rb_define_singleton_method(TiffFile, "to_tiff", (VALUE(*)(ANYARGS))method_tifffile_converter_to_tiff, 6);
|
237
|
+
}
|
data/lib/tifffile.rb
CHANGED
@@ -1,2 +1,28 @@
|
|
1
1
|
require 'tifffile/version'
|
2
2
|
require "tifffile/tifffile"
|
3
|
+
|
4
|
+
module TiffFile
|
5
|
+
|
6
|
+
include TiffFileVersion
|
7
|
+
|
8
|
+
# Will write a TIFF file +destination+, that contains +values+ matrix (in one channel), each sample has +sample_size+ in bytes (1, 2, 4 or 8), +sample_unsigned+.
|
9
|
+
# Also, image have +description+ and reference to +software+
|
10
|
+
def self.tiff2file(destination, values, sample_size=16, sample_unsigned=false, description=nil, software=nil)
|
11
|
+
self.to_tiff(destination.to_s, values, sample_size.to_i, sample_unsigned == true, description.to_s, software.to_s)
|
12
|
+
end
|
13
|
+
|
14
|
+
|
15
|
+
# Binary get TIFF file that contains +values+ matrix (in one channel), each sample has +sample_size+ in bytes (1, 2, 4 or 8), +sample_unsigned+.
|
16
|
+
# Also, image have +description+ and reference to +software+
|
17
|
+
def self.tiff2binary(values, sample_size=16, description=nil, software=nil)
|
18
|
+
file = Tempfile.new('tiff2binary')
|
19
|
+
file.close
|
20
|
+
|
21
|
+
tiff2file(file.path, values, sample_size, description, software)
|
22
|
+
|
23
|
+
data = File.read(file)
|
24
|
+
file.unlink
|
25
|
+
data
|
26
|
+
end
|
27
|
+
|
28
|
+
end
|
data/lib/tifffile/version.rb
CHANGED
@@ -1,3 +1,3 @@
|
|
1
|
-
module
|
2
|
-
VERSION = "0.0.
|
1
|
+
module TiffFileVersion
|
2
|
+
VERSION = "0.0.2"
|
3
3
|
end
|
metadata
CHANGED
@@ -1,14 +1,14 @@
|
|
1
1
|
--- !ruby/object:Gem::Specification
|
2
2
|
name: tifffile
|
3
3
|
version: !ruby/object:Gem::Version
|
4
|
-
version: 0.0.
|
4
|
+
version: 0.0.2
|
5
5
|
platform: ruby
|
6
6
|
authors:
|
7
7
|
- Kirill Makhonin
|
8
8
|
autorequire:
|
9
9
|
bindir: bin
|
10
10
|
cert_chain: []
|
11
|
-
date: 2016-03-
|
11
|
+
date: 2016-03-22 00:00:00.000000000 Z
|
12
12
|
dependencies: []
|
13
13
|
description: ''
|
14
14
|
email: kroks.rus@gmail.com
|
@@ -25,11 +25,12 @@ files:
|
|
25
25
|
- ".idea/tifffile-ruby.iml"
|
26
26
|
- LICENSE
|
27
27
|
- Rakefile
|
28
|
+
- analyzer.py
|
28
29
|
- ext/tifffile/extconf.rb
|
29
|
-
- ext/tifffile/tifffile.
|
30
|
-
- ext/tifffile/tifffile.h
|
30
|
+
- ext/tifffile/tifffile.cpp
|
31
31
|
- lib/tifffile.rb
|
32
32
|
- lib/tifffile/version.rb
|
33
|
+
- spec/tifffile_spec.rb
|
33
34
|
homepage: https://github.com/kirillmakhonin/tifffile-ruby
|
34
35
|
licenses:
|
35
36
|
- MIT
|
data/ext/tifffile/tifffile.c
DELETED
@@ -1,74 +0,0 @@
|
|
1
|
-
#include <tifffile.h>
|
2
|
-
|
3
|
-
struct my_malloc {
|
4
|
-
size_t size;
|
5
|
-
void *ptr;
|
6
|
-
};
|
7
|
-
|
8
|
-
static void
|
9
|
-
my_malloc_free(void *p) {
|
10
|
-
struct my_malloc *ptr = p;
|
11
|
-
|
12
|
-
if (ptr->size > 0)
|
13
|
-
free(ptr->ptr);
|
14
|
-
}
|
15
|
-
|
16
|
-
static VALUE
|
17
|
-
my_malloc_alloc(VALUE klass) {
|
18
|
-
VALUE obj;
|
19
|
-
struct my_malloc *ptr;
|
20
|
-
|
21
|
-
obj = Data_Make_Struct(klass, struct my_malloc, NULL, my_malloc_free, ptr);
|
22
|
-
|
23
|
-
ptr->size = 0;
|
24
|
-
ptr->ptr = NULL;
|
25
|
-
|
26
|
-
return obj;
|
27
|
-
}
|
28
|
-
|
29
|
-
static VALUE
|
30
|
-
my_malloc_init(VALUE self, VALUE size) {
|
31
|
-
struct my_malloc *ptr;
|
32
|
-
size_t requested = NUM2SIZET(size);
|
33
|
-
|
34
|
-
if (0 == requested)
|
35
|
-
rb_raise(rb_eArgError, "unable to allocate 0 bytes");
|
36
|
-
|
37
|
-
Data_Get_Struct(self, struct my_malloc, ptr);
|
38
|
-
|
39
|
-
ptr->ptr = malloc(requested);
|
40
|
-
|
41
|
-
if (NULL == ptr->ptr)
|
42
|
-
rb_raise(rb_eNoMemError, "unable to allocate %ld bytes", requested);
|
43
|
-
|
44
|
-
ptr->size = requested;
|
45
|
-
|
46
|
-
return self;
|
47
|
-
}
|
48
|
-
|
49
|
-
static VALUE
|
50
|
-
my_malloc_release(VALUE self) {
|
51
|
-
struct my_malloc *ptr;
|
52
|
-
|
53
|
-
Data_Get_Struct(self, struct my_malloc, ptr);
|
54
|
-
|
55
|
-
if (0 == ptr->size)
|
56
|
-
return self;
|
57
|
-
|
58
|
-
ptr->size = 0;
|
59
|
-
free(ptr->ptr);
|
60
|
-
|
61
|
-
return self;
|
62
|
-
}
|
63
|
-
|
64
|
-
void
|
65
|
-
Init_my_malloc(void) {
|
66
|
-
VALUE cMyMalloc;
|
67
|
-
|
68
|
-
cMyMalloc = rb_const_get(rb_cObject, rb_intern("TiffFile"));
|
69
|
-
|
70
|
-
rb_define_alloc_func(cMyMalloc, my_malloc_alloc);
|
71
|
-
rb_define_method(cMyMalloc, "initialize", my_malloc_init, 1);
|
72
|
-
rb_define_method(cMyMalloc, "free", my_malloc_release, 0);
|
73
|
-
}
|
74
|
-
|
data/ext/tifffile/tifffile.h
DELETED
@@ -1 +0,0 @@
|
|
1
|
-
#include <ruby.h>
|