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rename niiRead3() to niiReadFromMriFsStruct()
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@yhuang43
yhuang43 committed Feb 18, 2022
1 parent 0d02f83 commit 0b73664
Showing 1 changed file with 20 additions and 17 deletions.
37 changes: 20 additions & 17 deletions utils/mriio.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -136,7 +136,7 @@ static MRI *ximgRead(const char *fname, int read_volume);
static MRI *nifti1Read(const char *fname, int read_volume);
static int nifti1Write(MRI *mri, const char *fname);
static MRI *niiRead(const char *fname, int read_volume);
static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct);
static MRI *niiReadFromMriFsStruct(MRIFSSTRUCT *mrifsStruct);
static int niiWrite(MRI *mri, const char *fname);
static int itkMorphWrite(MRI *mri, const char *fname);
static int niftiQformToMri(MRI *mri, struct nifti_1_header *hdr);
Expand Down Expand Up @@ -687,7 +687,7 @@ MRI *mri_read(const char *fname, int type, int volume_flag, int start_frame, int
if (mrifsStruct == NULL)
return NULL;

mri = niiRead3(mrifsStruct);
mri = niiReadFromMriFsStruct(mrifsStruct);
if (mri != NULL && mri->ti < 0)
mri->ti = 0;

Expand All @@ -705,7 +705,7 @@ MRI *mri_read(const char *fname, int type, int volume_flag, int start_frame, int
if (mrifsStruct == NULL)
return NULL;

mri = niiRead3(mrifsStruct);
mri = niiReadFromMriFsStruct(mrifsStruct);

free(mrifsStruct->imgM);
free(mrifsStruct->tdti);
Expand Down Expand Up @@ -8792,12 +8792,15 @@ static MRI *niiRead(const char *fname, int read_volume)


/*------------------------------------------------------------------
niiRead3() - note: there are also nifti1Read() and niiRead(). Make sure to
niiReadFromMriFsStruct() - note: there are also nifti1Read() and niiRead(). Make sure to
edit all. Automatically detects whether an input is Ico7
and reshapes.
This function is used with DICOMRead3().
DICOMRead3() read/parse dicom files using dcm2niix_fswrapper.
MRIFSSTRUCT holds the parsing output from dcm2niix, which contains nifti header,
image data, acqusition parameters, and bvecs. See nii_dicom_batch.h for details.
-----------------------------------------------------------------*/
static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
static MRI *niiReadFromMriFsStruct(MRIFSSTRUCT *mrifsStruct)
{
MRI *mri, *mritmp;
int nslices;
Expand All @@ -8816,21 +8819,21 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
swapped_flag = TRUE;
swap_nifti_1_header(hdr);
if (hdr->dim[0] < 1 || hdr->dim[0] > 7) {
ErrorReturn(NULL, (ERROR_BADFILE, "niiRead3(): bad number of dimensions (%hd)", hdr->dim[0]));
ErrorReturn(NULL, (ERROR_BADFILE, "niiReadFromMriFsStruct(): bad number of dimensions (%hd)", hdr->dim[0]));
}
}

if (memcmp(hdr->magic, NII_MAGIC, 4) != 0) {
ErrorReturn(NULL, (ERROR_BADFILE, "niiRead3(): bad magic number"));
ErrorReturn(NULL, (ERROR_BADFILE, "niiReadFromMriFsStruct(): bad magic number"));
}

// if (hdr.dim[0] != 2 && hdr.dim[0] != 3 && hdr.dim[0] != 4){
if (hdr->dim[0] < 1 || hdr->dim[0] > 5) {
ErrorReturn(NULL, (ERROR_UNSUPPORTED, "niiRead3(): %hd dimensions; unsupported", hdr->dim[0]));
ErrorReturn(NULL, (ERROR_UNSUPPORTED, "niiReadFromMriFsStruct(): %hd dimensions; unsupported", hdr->dim[0]));
}

if (hdr->datatype == DT_NONE || hdr->datatype == DT_UNKNOWN) {
ErrorReturn(NULL, (ERROR_UNSUPPORTED, "niiRead3(): unknown or no data type; bailing out"));
ErrorReturn(NULL, (ERROR_UNSUPPORTED, "niiReadFromMriFsStruct(): unknown or no data type; bailing out"));
}
if (hdr->dim[4] == 0) {
printf("WARNING: hdr->dim[4] = 0 (nframes), setting to 1\n");
Expand All @@ -8848,7 +8851,7 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
space_units_factor = 1.0;
}
else
ErrorReturn(NULL, (ERROR_BADFILE, "niiRead3(): unknown space units %d", space_units));
ErrorReturn(NULL, (ERROR_BADFILE, "niiReadFromMriFsStruct(): unknown space units %d", space_units));

time_units = XYZT_TO_TIME(hdr->xyzt_units);
if (time_units == NIFTI_UNITS_SEC)
Expand All @@ -8871,7 +8874,7 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
hdr->slice_code != NIFTI_SLICE_ALT_INC && hdr->slice_code != NIFTI_SLICE_ALT_DEC &&
hdr->slice_code != NIFTI_SLICE_ALT_INC2 && hdr->slice_code != NIFTI_SLICE_ALT_DEC2) {
ErrorReturn(
NULL, (ERROR_UNSUPPORTED, "niiRead3(): unsupported slice timing pattern %d", hdr->slice_code));
NULL, (ERROR_UNSUPPORTED, "niiReadFromMriFsStruct(): unsupported slice timing pattern %d", hdr->slice_code));
}
}

Expand All @@ -8883,7 +8886,7 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
// put extra dims in frames
if (hdr->dim[0] > 4 && hdr->dim[5] > 0) nslices *= hdr->dim[5];
if (Gdiag_no > 0)
printf("niiRead3(): hdr->dim %d %d %d %d %d %d\n",
printf("niiReadFromMriFsStruct(): hdr->dim %d %d %d %d %d %d\n",
hdr->dim[0],
hdr->dim[1],
hdr->dim[2],
Expand Down Expand Up @@ -8934,19 +8937,19 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
else if (hdr->datatype == DT_DOUBLE) {
fs_type = MRI_FLOAT;
bytes_per_voxel = 8;
printf("niiRead3(): detected input as 64 bit double, reading in as 32 bit float\n");
printf("niiReadFromMriFsStruct(): detected input as 64 bit double, reading in as 32 bit float\n");
}
#if 0 // MRI_RBG not support in mghWrite
else if (hdr->datatype == DT_RGB) {
fs_type = MRI_UCHAR; //MRI_RGB;
bytes_per_voxel = 3;
printf("niiRead3(): DT_RGB, MRI_RGB\n");
printf("niiReadFromMriFsStruct(): DT_RGB, MRI_RGB\n");
}
#endif
else {
ErrorReturn(
NULL,
(ERROR_UNSUPPORTED, "niiRead3(): unsupported datatype %d (with scl_slope = 0)", hdr->datatype));
(ERROR_UNSUPPORTED, "niiReadFromMriFsStruct(): unsupported datatype %d (with scl_slope = 0)", hdr->datatype));
}
}
else {
Expand All @@ -8956,7 +8959,7 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)
hdr->datatype != DT_UINT32) {
ErrorReturn(
NULL,
(ERROR_UNSUPPORTED, "niiRead3(): unsupported datatype %d (with scl_slope != 0)", hdr->datatype));
(ERROR_UNSUPPORTED, "niiReadFromMriFsStruct(): unsupported datatype %d (with scl_slope != 0)", hdr->datatype));
}
fs_type = MRI_FLOAT;
bytes_per_voxel = 0; /* set below -- avoid the compiler warning */
Expand Down Expand Up @@ -9288,7 +9291,7 @@ static MRI *niiRead3(MRIFSSTRUCT *mrifsStruct)

return (mri);

} /* end niiRead3() */
} /* end niiReadFromMriFsStruct() */

/*------------------------------------------------------------------
niiWrite() - note: there is also an nifti1Write(). Make sure to
Expand Down

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