Practical assignment 1, basics of images

Diego Emiliano Tapia Cadena A01754796

Pt.1
Read and display the raw image "rx597x432.raw".

Id=fopen('rx597x432.raw','r');
I=fread(Id, [432 597],'*uint8');
image(I), colormap(gray(256)), axis image

I=I';

Read and display the image "slice.bmp".

slice = imread('slice.bmp');
whos slice

Name Size Bytes Class Attributes

slice 503x413 207739 uint8

figure, image(slice)
colormap(gray(256))
axis image

1
Read the image "rxcerv.pcx" and display it using first the command image, and

then the command imagesc. What’s the difference?

I2=imread('rxcerv.pcx');
image(I2),colormap(gray(256)), axis image

figure,imagesc(I2),colormap(gray(256)),axis image

2
There's no difference because of the "imagesc", it's the same color palette used in both images (uint8).

Repeat the point 5, this time using the image “abdominal.png”. What function suits

better to display the image?

I3=imread('abdominal.png');
image(I3),colormap(gray(256)), axis image

figure,imagesc(I3),colormap(gray(256)),axis image

3
The difference between images, is the white contrast, it works better for the "imagesc" function.

Open and visualize the RGB image “tumorRGB.jpg”, What´s its size? Display it

using the command imshow

I4=imread('tumorRGB.jpg');
image(I4)

imshow(I4)

4
 figure,image(I4)

Read the image “polypRGB.jpg” and display each of its components in a different

window.

I5=imread('polypRGB.jpg','jpg');
polypR=I5(:,:,1);
polypG=I5(:,:,2);
polypB=I5(:,:,3);
temp=0:(1/255):1;
zero=zeros(256,1);
figure(9)
imagesc(I5); title('RGB');

5
figure(10)
imagesc(polypR);colormap([temp' zero zero]);
title('Red')

figure(11)
imagesc(polypG);colormap([zero temp' zero]);
title('Green')

6
 figure(12)
imagesc(polypB);colormap([zero zero temp']);
title('Blue');

Read the RGB image “dancersRGB.jpg”, transform it into a grayscale image and

visualize the result. To Transform an RGB image into a grayscale one you must

multiply each of the RGB component by a coefficient and then add all of them, this

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is:

I6=imread('dancersRGB.jpeg');
imshow(I6)

I6rgb=rgb2gray(I6);
max(I6rgb(:));
min(I6rgb(:));
subplot(1,2,1),imshow(I6)
subplot(1,2,2),imshow(I6rgb)

8
Visualize the transformed image using the different predefined color maps in

matlab.

figure,imagesc(I6rgb),axis image
colormap cool

9
figure,imagesc(I6rgb),axis image
colormap copper

figure,imagesc(I6rgb),axis image
colormap parula

figure,imagesc(I6rgb),axis image
colormap pink

10
Read the dicom image “vrie.dcm” using the command dicomread.

I7=dicomread('vrie.dcm');
size(I7)

ans = 1×4
64 64 1 16

I7=squeeze(I7);
imagesc(I7(:,:,1)),colormap('hot')

11
 for i=1:16
subplot(4,4,i), imagesc(I7(:,:,i)),colormap('hot')
end

Dicom files contain “metadata” related to the imaging study performed. To retrieve

this information matlab has the function dicominfo. Display the metadata of the

DICOM file "vrie.dcm".

infod=dicominfo('vrie.dcm')

Warning: File and dictionary VR values do not match for attribute "CodeMeaning" (0008,0104).
Expected: LO. Found: SH. Consider setting the 'UseDictionaryVR' parameter to true.
infod = struct with fields:
Filename: '/Users/diegotapia/Documents/MATLAB/vrie.dcm'
FileModDate: '08-Jun-2005 14:52:40'
FileSize: 136074
Format: 'DICOM'
FormatVersion: 3
Width: 64
Height: 64
BitDepth: 16
ColorType: 'grayscale'
FileMetaInformationGroupLength: 200
FileMetaInformationVersion: [2×1 uint8]
MediaStorageSOPClassUID: '1.2.840.10008.5.1.4.1.1.20'
MediaStorageSOPInstanceUID: '1.2.840.113619.2.84.21524.416529.63.75.1043768211.4'
TransferSyntaxUID: '1.2.840.10008.1.2.1'
ImplementationClassUID: '1.2.840.113619.6.112'
ImplementationVersionName: 'eNTEGRA 2.5202'
SourceApplicationEntityTitle: 'PROCE'
IdentifyingGroupLength: 516
ImageType: 'DERIVED\PRIMARY\GATED\EMISSION'
InstanceCreationDate: '20050608'
InstanceCreationTime: '135240.0000'

12
 InstanceCreatorUID: '1.2.840.113619.6.112'
SOPClassUID: '1.2.840.10008.5.1.4.1.1.20'
SOPInstanceUID: '1.2.840.113619.2.84.21524.416529.63.75.1043768211.4'
StudyDate: '20030128'
SeriesDate: '20030128'
AcquisitionDate: '20030128'
ContentDate: '20030128'
StudyTime: '093556.00'
SeriesTime: '093829.00'
AcquisitionTime: '093829.00'
ContentTime: '093829.00'
AccessionNumber: ''
Modality: 'NM'
Manufacturer: 'GE MEDICAL SYSTEMS'
InstitutionName: 'Instituto Nacional de Cardiologia'
ReferringPhysicianName: [1×1 struct]
StationName: 'sala1'
StudyDescription: 'Gated Blood Pool'
SeriesDescription: '45 LAO'
NameOfPhysiciansReadingStudy: [1×1 struct]
OperatorsName: [1×1 struct]
ManufacturerModelName: 'MILLENNIUM MPT'
Private_0009_GroupLength: 488
Private_0009_10xx_Creator: 'GEMS_GENIE_1'
Private_0009_1001: 'GEMS_GENIE'
Private_0009_1010: 'MULTIGATED'
Private_0009_1011: 4105
Private_0009_1012: 1
Private_0009_101e: '1.2.840.113619.2.84.21524.416529.63.75.1043768211.4'
Private_0009_1020: '45 LAO'
Private_0009_1021: 1
Private_0009_1022: ''
Private_0009_1023: 2
Private_0009_1024: 60000
Private_0009_1025: 1000
Private_0009_1026: 1
Private_0009_1027: 1
Private_0009_1028: 1
Private_0009_1029: 16
Private_0009_102a: 0
Private_0009_102b: ''
Private_0009_102c: ''
Private_0009_102d: 0
Private_0009_102e: 0
Private_0009_102f: 0
Private_0009_1037: 58
Private_0009_103a: 100
Private_0009_1040: [1×1 struct]
Private_0009_1041: 1
Private_0009_1042: '20030128'
Private_0009_1043: '093647.00'
Private_0009_1045: '1.2.840.113619.2.84.21524.416529.63.75.1043768211.4'
PatientGroupLength: 112
PatientName: [1×1 struct]
PatientID: '00'
PatientBirthDate: ''
PatientSex: 'M'
OtherPatientIDs: ''
OtherPatientNames: [1×1 struct]
PatientSize: 0
PatientWeight: 0
EthnicGroup: ''
Occupation: ''
Private_0011_GroupLength: 654

13
 Private_0011_10xx_Creator: 'GEMS_GENIE_1'
Private_0011_100a: 3
Private_0011_100b: 300280
Private_0011_100c: 238
Private_0011_100d: 'Tc99m'
Private_0011_1010: ''
Private_0011_1011: 0
Private_0011_1012: '45 LAO'
Private_0011_1013: 11
Private_0011_1014: ''
Private_0011_1015: 1
Private_0011_1016: 1
Private_0011_1017: 1
Private_0011_1018: 0
Private_0011_1019: 181.1830
Private_0011_101a: 1
Private_0011_101f: 0
Private_0011_1026: 0
Private_0011_1027: [2×1 int32]
Private_0011_1028: [2×1 int32]
Private_0011_102c: 0
Private_0011_102d: 0
Private_0011_102e: 0
Private_0011_102f: 32767
Private_0011_1030: '45 LAO'
Private_0011_1031: '**'
Private_0011_1032: '**'
Private_0011_1033: 'ECOR'
Private_0011_1034: 'Tc99m'
Private_0011_1035: 'PMT'
Private_0011_1036: '**'
Private_0011_1037: '**'
Private_0011_1038: 108
Private_0011_1039: 0
Private_0011_103a: 5
Private_0011_103b: 1
Private_0011_103c: 0
Private_0011_103f: 9
Private_0011_1040: 'current'
Private_0011_1041: 0
Private_0011_1042: 0
Private_0011_1043: 0
Private_0011_1044: 2048
Private_0011_1045: 4096
Private_0011_1046: 2
Private_0011_1050: '45 LAO'
Private_0011_1055: 1
Private_0011_1056: 1
Private_0011_1057: [2×1 double]
Private_0013_GroupLength: 84
Private_0013_10xx_Creator: 'GEMS_GENIE_1'
Private_0013_1010: [2×1 double]
Private_0013_1011: 4
Private_0013_1012: 0
Private_0013_1015: 0
Private_0015_GroupLength: 32
Private_0015_10xx_Creator: 'GEMS_GENIE_1'
Private_0015_1017: 0
AcquisitionGroupLength: 196
BodyPartExamined: 'HEART'
CountsAccumulated: 4051048
AcquisitionTerminationCondition: 'TIME'
DeviceSerialNumber: '192.168.2.1'
SoftwareVersions: '2.7: FW 3-1_01'

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 ProtocolName: 'Gated Blood Pool'
TriggerSourceOrType: 'EKG'
BeatRejectionFlag: 'Y'
SkipBeats: 1
HeartRate: 57
TableHeight: 0
TableTraverse: 0
CountRate: 16709
PatientPosition: 'FFS'
Private_0019_GroupLength: 32
Private_0019_10xx_Creator: 'GEMS_GENIE_1'
Private_0019_105f: [1×1 struct]
RelationshipGroupLength: 242
StudyInstanceUID: '1.2.840.113619.2.84.21524.416529.4.70.1043768156.1'
SeriesInstanceUID: '1.2.840.113619.2.84.21524.416529.63.69.1043768210.3'
StudyID: 'MULTIGATED'
SeriesNumber: 3034
InstanceNumber: 11637
FrameOfReferenceUID: '1.2.840.113619.2.84.21524.416529.63.69.1043768210.3.3034'
Laterality: ''
PositionReferenceIndicator: ''
ImagePresentationGroupLength: 226
SamplesPerPixel: 1
PhotometricInterpretation: 'MONOCHROME2'
NumberOfFrames: 16
FrameIncrementPointer: [84 16 84 32 84 96 84 112]
Rows: 64
Columns: 64
PixelSpacing: [2×1 double]
BitsAllocated: 16
BitsStored: 16
HighBit: 15
PixelRepresentation: 1
SmallestImagePixelValue: 0
LargestImagePixelValue: 278
SmallestPixelValueInSeries: 0
LargestPixelValueInSeries: 278
WindowCenter: 139
WindowWidth: 278
Private_0033_GroupLength: 80
Private_0033_10xx_Creator: 'GEMS_GENIE_1'
Private_0033_1007: '1.2.840.113619.2.84.21524.416529.63.75.1043768211.4'
Unknown_0040_0000: 12
RequestAttributesSequence: [1×1 struct]
NuclearAcquisitionGroupLength: 1264
EnergyWindowVector: [16×1 uint16]
NumberOfEnergyWindows: 1
EnergyWindowInformationSequence: [1×1 struct]
RadiopharmaceuticalInformationSequence: [1×1 struct]
DetectorVector: [16×1 uint16]
NumberOfDetectors: 1
DetectorInformationSequence: [1×1 struct]
RRIntervalVector: [16×1 uint16]
NumberOfRRIntervals: 1
GatedInformationSequence: [1×1 struct]
TimeSlotVector: [16×1 uint16]
NumberOfTimeSlots: 16
ImageID: '45 LAO'
PatientOrientationCodeSequence: [1×1 struct]
PatientGantryRelationshipCodeSequence: [1×1 struct]
Private_0055_GroupLength: 528
Private_0055_10xx_Creator: 'GEMS_GENIE_1'
Private_0055_1012: [1×1 struct]
Private_0055_1022: [1×1 struct]

15
 Private_0055_1062: [1×1 struct]
Private_0055_1065: [1×1 struct]
PixelDataGroupLength: 131084

Determine the number of images in the file "Rx_knee_foot.tif", show the

information of image number 3.

I8 = imfinfo('Rx_knee_foot.tif','tiff');
size(I8)

ans = 1×2
4 1

I8(3)

ans = struct with fields:

Filename: '/Users/diegotapia/Documents/MATLAB/Rx_knee_foot.tif'
FileModDate: '20-Feb-2004 13:03:18'
FileSize: 677820
Format: 'tif'
FormatVersion: []
Width: 576
Height: 297
BitDepth: 8
ColorType: 'indexed'
FormatSignature: [73 73 42 0]
ByteOrder: 'little-endian'
NewSubFileType: 0
BitsPerSample: 8
Compression: 'Uncompressed'
PhotometricInterpretation: 'RGB Palette'
StripOffsets: 373970
SamplesPerPixel: 1
RowsPerStrip: 297
StripByteCounts: 171072
XResolution: 97
YResolution: 97
ResolutionUnit: 'Inch'
Colormap: [256×3 double]
PlanarConfiguration: 'Chunky'
TileWidth: []
TileLength: []
TileOffsets: []
TileByteCounts: []
Orientation: 1
FillOrder: 1
GrayResponseUnit: 0.0100
MaxSampleValue: 255
MinSampleValue: 0
Thresholding: 1
Offset: 372232

Open all of the images in the file “Rx_knee_foot.tif” and display them in the same

window. (use the function subplot).

I9=imread('Rx_knee_foot.tif',1);
I10=imread('Rx_knee_foot.tif',2);
I11=imread('Rx_knee_foot.tif',3);
I12=imread('Rx_knee_foot.tif',4);
figure,

16
 subplot(2,2,1), imshow(I9);
subplot(2,2,2), imshow(I10);
subplot(2,2,3), imshow(I11);
subplot(2,2,4), imshow(I12);

Pt. 2
Write a matlab function whose input argument is an image in a matlab supported

format and its output argument is the same image in a raw format.
inputI: MATLAB supported image format, outputFN; Name for the output raw file, get image size, and convert
to .Raw, finally display to confirm the process was OK.

CTR('rosa.jpg', 'rosa2.raw'); %No sé qué significa el error que manda aquí,

pero si hace el "rosa2.raw"

Error using '

TRANSPOSE does not support N-D arrays. Use PAGETRANSPOSE/PAGECTRANSPOSE to transpose pages or
PERMUTE to reorder dimensions of N-D arrays.

Error in CTR (line 7)

fwrite(fid, img', 'uint8');

Id=fopen('rosa2.raw','r');
I13=fread(Id,[432 597],'*uint8');
figure,
image(I13),colormap(gray(256)), axis image
I13=I13';

Create a function that makes the same task as the command imresize, to reduce the

size of an input image by a factor of ½. (Cannot use imresize function).

17
 I14=imread('rosa.jpg');
figure, imshow(I14)
ri = ci('rosa.jpg', 0.5)
imshow(ri)

Figure out the right way to visualize the indexed image “cta_scan_index.bmp”

using matlab commands.

I15 = imread('cta_scan_index.bmp');
[b,bmap]=imread('cta_scan_index.bmp');
figure,
subplot(1, 2, 1);
imshow(I15);
subplot(1, 2, 2);
imshow(b,bmap)

18