Merge pull request #72 from elgw/dev

Fix for issue #70

CHANGELOG.md

@@ -1,5 +1,16 @@
 # CHANGELOG
 
+## 0.4.3
+- Fixed [issue #70](https://github.com/elgw/deconwolf/issues/70) which
+  affected windows builds only.
+
+- Dw will now give a error message if the log file can't be opened
+  instead of quietly crashing.
+
+- Disabled some debug code that caused dw to write the file
+  (`one.tif`) every time that is was run. It has been doing so since
+  version 0.4.1.
+
 ## 0.4.2
 - VkFFT upgraded from v1.3.3 to v1.3.4.
 - Fixed an issue preventing anything than `--bq 0` to be used on

README.md

@@ -1,4 +1,4 @@
-# deconwolf v0.4.2
+# deconwolf v0.4.3
 
 **deconwolf**[^9] is a software for 3-D deconvolution of fluorescent wide-field
 images:

src/dw.c

@@ -934,19 +934,20 @@ void dw_argparsing(int argc, char ** argv, dw_opts * s)
     }
 
 
+    /* Set s->outFile and s->outFolder based on s->imFile */
     if(s->outFile == NULL)
-    {
-        /* Set s->outFile and s->outFolder based on s->imFile */
-        char * dname = dw_dirname(s->imFile);
-        char * bname = dw_basename(s->imFile);
-        s->outFile = malloc(strlen(dname) + strlen(bname) + strlen(s->prefix) + 10);
-        assert(s->outFile != NULL);
-        sprintf(s->outFile, "%s%c%s_%s", dname, FILESEP, s->prefix, bname);
+    {        
+        s->outFile = dw_prefix_file(s->imFile, s->prefix);
+
+        char * dname = dw_dirname(s->imFile);        
         s->outFolder = malloc(strlen(dname) + 16);
         assert(s->outFolder != NULL);
-        sprintf(s->outFolder, "%s%c", dname, FILESEP);
-        free(bname);
+        sprintf(s->outFolder, "%s%c", dname, FILESEP);      
         free(dname);
+        if(s->verbosity > 1)
+        {
+            printf("outFile: %s, outFolder: %s\n", s->outFile, s->outFolder);
+        }
     } else {
         char * dname = dw_dirname(s->outFile);
         free(s->outFolder);
@@ -1980,6 +1981,14 @@ float * psf_makeOdd(float * psf, int64_t * pM, int64_t * pN, int64_t *pP)
 void dcw_init_log(dw_opts * s)
 {
     s->log = fopen(s->logFile, "w");
+    if (s->log == NULL)
+    {
+        fprintf(stderr, "Unable to open %s for writing\n", s->logFile);
+        fprintf(stderr,
+            "Please check that you have permissions to write to the folder\n"
+            "and that the drive is not full\n");        
+        exit(EXIT_FAILURE);
+    }
     assert(s->log != NULL);
     show_time(s->log);
     dw_opts_fprint(s->log, s);
@@ -2072,6 +2081,8 @@ fftwf_complex * initial_guess(const int64_t M, const int64_t N, const int64_t P,
             }
         }
     }
+    //printf("writing to one.tif");
+    //fim_tiff_write_float("one.tif", one, NULL, wM, wN, wP);
     //  writetif("one.tif", one, wM, wN, wP);
 
     fftwf_complex * Fone = fft(one, wM, wN, wP);

src/dw_util.c

@@ -85,24 +85,26 @@ void dw_gettime(struct timespec * t)
 
 char * dw_dirname(const char * path)
 {
-    #ifdef WINDOWS
+#ifdef WINDOWS
     size_t maxlen = strlen(path)+1;
     char * drive = malloc(maxlen);
     char * dir = malloc(maxlen);
 
     _splitpath(path, drive, dir, NULL, NULL);
     char * outpath = malloc(maxlen);
     _makepath(outpath, drive, dir, NULL, NULL);
+    // Adds a trailing '\'
     free(drive);
     free(dir);
     return outpath;
-    #else
+#else
     char * t = strdup(path);
     char * _dir = dirname(t); // should not be freed
+    // Does not add a trailing '/'
     char * dir = strdup(_dir);
     free(t);
     return dir;
-    #endif
+#endif
 }
 
 char * dw_basename(const char * path)
@@ -128,11 +130,11 @@ char * dw_basename(const char * path)
 
 char * dw_getcwd(char * buf, size_t size)
 {
-    #ifdef WINDOWS
+#ifdef WINDOWS
     return _getcwd(buf, size);
-    #else
+#else
     return getcwd(buf, size);
-    #endif
+#endif
 }
 
 int ptr_alignment_B(const void * p)
@@ -354,7 +356,40 @@ int getline(char **lineptr, size_t *n, FILE *stream)
 char *
 dw_prefix_file(const char * inFile, const char * prefix)
 {
+#ifdef WINDOWS
+
+    char* drive = calloc(strlen(inFile) + 16, 1);
+    char* dir = calloc(strlen(inFile) + 16, 1);
+    char* fname = calloc(strlen(inFile) + 16, 1);
+    char* ext = calloc(strlen(inFile) + 16, 1);
+
+    _splitpath(
+        inFile,
+        drive,
+        dir,
+        fname,
+        ext
+    );
+
+    char* pre_fname = calloc(strlen(fname) + strlen(prefix) + 16, 1);
+    sprintf(pre_fname, "%s_%s", prefix, fname);
+    char* outFile = calloc(strlen(inFile) + strlen(prefix) + 128, 1);
+
+    _makepath(
+        outFile,
+        drive,
+        dir,
+        pre_fname,
+        ext
+    );
 
+    free(drive);
+    free(dir);
+    free(fname);
+    free(pre_fname);
+    free(ext);
+    return outFile;
+#else
     char * dname = dw_dirname(inFile);
     assert(dname != NULL);
     char * fname = dw_basename(inFile);
@@ -373,6 +408,7 @@ dw_prefix_file(const char * inFile, const char * prefix)
     free(fname);
 
     return outFile;
+#endif
 }
 
 float abbe_res_xy(float lambda, float NA)

src/dw_version.h

@@ -2,7 +2,7 @@
 
 #define DW_VERSION_MAJOR "0"
 #define DW_VERSION_MINOR "4"
-#define DW_VERSION_PATCH "2"
+#define DW_VERSION_PATCH "3"
 #define deconwolf_version DW_VERSION_MAJOR "." \
     DW_VERSION_MINOR "." \
     DW_VERSION_PATCH