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R8218/Excel2SQL/CTfromExcel.m
233813c10a01Bashardoust_SystCoord

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CTfromExcel.m
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function [CT, scapula, glenoid, glenoid_density, humerus, muscle] = CTfromExcel(shoulder, patient, rawExcel)
% ctFromExcel build the ct structure array from the excelRaw, patient and
% shoulder structure array.
% ct contains all data directly related to the imaging
fprintf('\nGet CT & glenoid from Excel...');
% define CT structure array
CT = struct(...
'CT_id', [], ...
'shoulder_id', [], ...
'date', [], ...
'kernel', [], ...
'pixel_size', [], ...
'slice_spacing', [], ...
'slice_thickness', [], ...
'tension', [], ...
'current', [], ...
'manufacturer', [], ...
'model', [], ...
'institution', [], ...
'folder_name', [] ...
);
% define scapula array
scapula = struct(...
'CT_id' , [], ...
'CTangle', []...
);
% define glenoid structure array
glenoid = struct(...
'CT_id', [], ...
'radius', [], ...
'sphericity', [], ...
'biconcave', [], ...
'depth', [], ...
'width', [], ...
'height', [], ...
'version_amp', [], ...
'version_orient', [], ...
'center_PA', [], ...
'center_IS', [], ...
'center_ML', [], ...
'version', [], ...
'inclination', [], ...
'version_2D', [], ...
'walch_class', [] ...
);
% define glenoid_density structure array
glenoid_density = struct(...
'CT_id',[], ...
'CO' ,[], ...
'SC' ,[], ...
'ST' ,[], ...
'T1' ,[], ...
'T2' ,[], ...
'T3' ,[], ...
'RE' ,[] ...
);
% define humerus structure array
humerus = struct(...
'CT_id' ,[], ...
'joint_radius' ,[], ...
'head_radius' ,[], ...
'SHsublux_ampl' ,[], ...
'SHsublux_orient',[], ...
'GHsublux_ampl' ,[], ...
'GHsublux_orient',[], ...
'SHsublux_2D' ,[], ...
'GHsublux_2D' ,[] ...
);
%define muscle structure array
muscle = struct(...
'CT_id',[], ...
'SSA' ,[],...
'SSI' ,[],...
'SSO' ,[],...
'SSD' ,[],...
'ISA' ,[],...
'ISI' ,[],...
'ISO' ,[],...
'ISD' ,[],...
'SCA' ,[],...
'SCI' ,[],...
'SCO' ,[],...
'SCD' ,[],...
'TMA' ,[],...
'TMI' ,[],...
'TMO' ,[],...
'TMD' ,[] ...
);
% get column of variables
header = rawExcel(1,:);
sCase_id_col = find(strcmp([header],'sCase.id'));
IPP_col = find(strcmp([header],'patient.IPP'));
side_col = find(strcmp([header],'shoulder.side'));
CT_date_col = find(strcmp([header],'CT.date'));
CT_kernel_col = find(strcmp([header],'CT.kernel'));
CT_pixel_size_col = find(strcmp([header],'CT.pixel_size'));
CT_slice_spacing_col = find(strcmp([header],'CT.slice_spacing'));
CT_slice_thickness_col = find(strcmp([header],'CT.slice_thickness'));
CT_tension_col = find(strcmp([header],'CT.tension'));
CT_current_col = find(strcmp([header],'CT.current'));
CT_manufacturer_col = find(strcmp([header],'CT.manufacturer'));
CT_model_col = find(strcmp([header],'CT.model'));
CT_institution_col = find(strcmp([header],'CT.institution'));
scapula_CTangle_col = find(strcmp([header],'scapula.CTangle'));
glenoid_radius_col = find(strcmp([header],'glenoid.radius'));
% glenoid_sphericity_col = find(strcmp([header],'glenoid.sphericity'));
% glenoid_biconcave_col = find(strcmp([header],'glenoid.biconcave'));
glenoid_depth_col = find(strcmp([header],'glenoid.depth'));
glenoid_width_col = find(strcmp([header],'glenoid.width'));
glenoid_height_col = find(strcmp([header],'glenoid.height'));
glenoid_version_amp_col = find(strcmp([header],'glenoid.version_amp'));
glenoid_version_orient_col = find(strcmp([header],'glenoid.version_orient'));
glenoid_center_PA_col = find(strcmp([header],'glenoid.center_PA'));
glenoid_center_IS_col = find(strcmp([header],'glenoid.center_IS'));
glenoid_center_ML_col = find(strcmp([header],'glenoid.center_ML'));
glenoid_version_col = find(strcmp([header],'glenoid.version'));
glenoid_inclination_col = find(strcmp([header],'glenoid.inclination'));
glenoid_version_2D_col = find(strcmp([header],'glenoid.version_2D'));
glenoid_walch_class_col = find(strcmp([header],'glenoid.walch_class'));
glenoid_density_CO_col = find(strcmp([header],'glenoid_density.CO'));
glenoid_density_SC_col = find(strcmp([header],'glenoid_density.SC'));
glenoid_density_ST_col = find(strcmp([header],'glenoid_density.ST'));
glenoid_density_T1_col = find(strcmp([header],'glenoid_density.T1'));
glenoid_density_T2_col = find(strcmp([header],'glenoid_density.T2'));
glenoid_density_T3_col = find(strcmp([header],'glenoid_density.T3'));
glenoid_density_RE_col = find(strcmp([header],'glenoid_density.RE'));
humerus_joint_radius_col = find(strcmp([header],'humerus.joint_radius'));
humerus_head_radius_col = find(strcmp([header],'humerus.head_radius'));
humerus_SHsublux_ampl_col = find(strcmp([header],'humerus.SHsublux_ampl'));
humerus_SHsublux_orient_col = find(strcmp([header],'humerus.SHsublux_orient'));
humerus_GHsublux_ampl_col = find(strcmp([header],'humerus.GHsublux_ampl'));
humerus_GHsublux_orient_col = find(strcmp([header],'humerus.GHsublux_orient'));
humerus_SHsublux_2D_col = find(strcmp([header],'humerus.SHsublux_2D'));
humerus_GHsublux_2D_col = find(strcmp([header],'humerus.GHsublux_2D'));
muscle_SSA_col = find(strcmp([header],'muscle.SSA'));
muscle_SSI_col = find(strcmp([header],'muscle.SSI'));
muscle_SSO_col = find(strcmp([header],'muscle.SSO'));
muscle_SSD_col = find(strcmp([header],'muscle.SSD'));
muscle_ISA_col = find(strcmp([header],'muscle.ISA'));
muscle_ISI_col = find(strcmp([header],'muscle.ISI'));
muscle_ISO_col = find(strcmp([header],'muscle.ISO'));
muscle_ISD_col = find(strcmp([header],'muscle.ISD'));
muscle_SCA_col = find(strcmp([header],'muscle.SCA'));
muscle_SCI_col = find(strcmp([header],'muscle.SCI'));
muscle_SCO_col = find(strcmp([header],'muscle.SCO'));
muscle_SCD_col = find(strcmp([header],'muscle.SCD'));
muscle_TMA_col = find(strcmp([header],'muscle.TMA'));
muscle_TMI_col = find(strcmp([header],'muscle.TMI'));
muscle_TMO_col = find(strcmp([header],'muscle.TMO'));
muscle_TMD_col = find(strcmp([header],'muscle.TMD'));
% initialize counters
[rowN, ~] = size(rawExcel);
CT_id = 0;
CT_idx = 0;
scapula_idx = 0;
glenoid_idx = 0;
glenoid_density_idx = 0;
humerus_idx = 0;
muscle_idx = 0;
% loop over rows of Excel table
for row_idx = 2:rowN
row = rawExcel(row_idx, :); % get the entire row
sCaseE = row{sCase_id_col};
if ~isnan(sCaseE) % check that this sCase is not empty
IPP = row{IPP_col}; % IPP of the patient
patient_idx = find([patient.IPP] == IPP);
% get patient index of this sCase
% this patient should already exist in patient structure array and
% should be unique
if ~isempty(patient_idx)
patient_id = patient(patient_idx).patient_id; % get patient_id
shoulder_idx = find([shoulder.patient_id] == patient_id); % get shoulder_id
% should be 1 or 2 (R/L), but not 0 (test it however)
shoulder_idxN = length(shoulder_idx);
side = row{side_col};
switch shoulder_idxN
case 0
% this sCase patient is not in the shoulder array
% report an error (probably not side identified)
fprintf('\nsCase %s not in shoulder array', sCaseE);
addCT = 0;
case 1
% this sCase patient has 1 match in the shoulder array
% so we have to check side
if side == shoulder(shoulder_idx).side
shoulder_id = shoulder(shoulder_idx).shoulder_id;
addCT = 1;
else
% not same side so report a problem, probably side not
% defined
fprintf('\nsCase %s in shoulder array but not same side', sCaseE);
end
case 2
% both shoulder sides of this patient are in the
% shoulder array, so we have to check side
if side == shoulder(shoulder_idx(1)).side
shoulder_id = shoulder(shoulder_idx(1)).shoulder_id;
addCT = 1;
else
if side == shoulder(shoulder_idx(2)).side
shoulder_id = shoulder(shoulder_idx(2)).shoulder_id;
addCT = 1;
end
end
end
% check if CT kernel is defined
kernel = row{CT_kernel_col};
if isnan(kernel)
addCT = 0;
end
if addCT % add CT to the array
CT_id = CT_id + 1;
CT_idx = CT_id;
CT_date = row{CT_date_col};
CT_date = datetime(CT_date,'ConvertFrom','excel','InputFormat','dd.MM.yyyy');
CT_date.Format = 'yyyy-MM-dd';
CT(CT_idx).CT_id = CT_id;
CT(CT_idx).shoulder_id = shoulder_id;
CT(CT_idx).date = CT_date;
CT(CT_idx).kernel = row{CT_kernel_col};
CT(CT_idx).pixel_size = row{CT_pixel_size_col};
CT(CT_idx).slice_spacing = row{CT_slice_spacing_col};
CT(CT_idx).slice_thickness = row{CT_slice_thickness_col};
CT(CT_idx).tension = row{CT_tension_col};
CT(CT_idx).current = row{CT_current_col};
CT(CT_idx).manufacturer = row{CT_manufacturer_col};
CT(CT_idx).model = row{CT_model_col};
CT(CT_idx).institution = row{CT_institution_col};
CT(CT_idx).folder_name = sCaseE;
% check for adding in scapula structure array
CTangle = row{scapula_CTangle_col};
if ~isnan(CTangle)
scapula_idx = scapula_idx + 1;
scapula(scapula_idx).CT_id = CT_id;
scapula(scapula_idx).CTangle = CTangle;
end
% check for adding in glenoid structure array
radius = row{glenoid_radius_col};
if ~isnan(radius)
% Assumes that all glenoid data are present & valid is
% radius is defined
glenoid_idx = glenoid_idx + 1;
% sphericity = row{glenoid_sphericity_col};
% biconcave = row{glenoid_biconcave_col};
depth = row{glenoid_depth_col};
width = row{glenoid_width_col};
height = row{glenoid_height_col};
version_amp = row{glenoid_version_amp_col};
version_orient = row{glenoid_version_orient_col};
center_PA = row{glenoid_center_PA_col};
center_IS = row{glenoid_center_IS_col};
center_ML = row{glenoid_center_ML_col};
version = row{glenoid_version_col};
inclination = row{glenoid_inclination_col};
version_2D = row{glenoid_version_2D_col};
walch_class = row{glenoid_walch_class_col};
glenoid(glenoid_idx).CT_id = CT_id;
glenoid(glenoid_idx).radius = radius;
% glenoid(glenoid_idx).sphericity = sphericity;
% glenoid(glenoid_idx).biconcave = biconcave;
glenoid(glenoid_idx).depth = depth;
glenoid(glenoid_idx).width = width;
glenoid(glenoid_idx).height = height;
glenoid(glenoid_idx).version_amp = version_amp;
glenoid(glenoid_idx).version_orient = version_orient;
glenoid(glenoid_idx).center_PA = center_PA;
glenoid(glenoid_idx).center_IS = center_IS;
glenoid(glenoid_idx).center_ML = center_ML;
glenoid(glenoid_idx).version = version;
glenoid(glenoid_idx).inclination = inclination;
glenoid(glenoid_idx).version_2D = version_2D;
glenoid(glenoid_idx).walch_class = walch_class;
end
% check for adding in glenoid_density structure array
CO = row{glenoid_density_CO_col};
if ~isnan(CO)
% Assumes that all glenoid_density data are present & valid is
% CO is defined. RE can be empty
glenoid_density_idx = glenoid_density_idx + 1;
SC = row{glenoid_density_SC_col};
ST = row{glenoid_density_ST_col};
T1 = row{glenoid_density_T1_col};
T2 = row{glenoid_density_T2_col};
T3 = row{glenoid_density_T3_col};
RE = row{glenoid_density_RE_col};
glenoid_density(glenoid_density_idx).CT_id = CT_id;
glenoid_density(glenoid_density_idx).CO = CO;
glenoid_density(glenoid_density_idx).SC = SC;
glenoid_density(glenoid_density_idx).ST = ST;
glenoid_density(glenoid_density_idx).T1 = T1;
glenoid_density(glenoid_density_idx).T2 = T2;
glenoid_density(glenoid_density_idx).T3 = T3;
glenoid_density(glenoid_density_idx).RE = RE;
end
% check for adding in humerus structure array
head_radius = row{humerus_head_radius_col};
if ~isnan(head_radius)
% Assumes that all humerus data are present & valid is
% head_radius is defined.
humerus_idx = humerus_idx + 1;
joint_radius = row{humerus_joint_radius_col};
SHsublux_ampl = row{humerus_SHsublux_ampl_col};
SHsublux_orient = row{humerus_SHsublux_orient_col};
GHsublux_ampl = row{humerus_GHsublux_ampl_col};
GHsublux_orient = row{humerus_GHsublux_orient_col};
SHsublux_2D = row{humerus_SHsublux_2D_col};
GHsublux_2D = row{humerus_GHsublux_2D_col};
humerus(humerus_idx).CT_id = CT_id;
humerus(humerus_idx).head_radius = head_radius;
humerus(humerus_idx).joint_radius = joint_radius;
humerus(humerus_idx).SHsublux_ampl = SHsublux_ampl;
humerus(humerus_idx).SHsublux_orient = SHsublux_orient;
humerus(humerus_idx).GHsublux_ampl = GHsublux_ampl;
humerus(humerus_idx).GHsublux_orient = GHsublux_orient;
humerus(humerus_idx).SHsublux_2D = SHsublux_2D;
humerus(humerus_idx).GHsublux_2D = GHsublux_2D;
end
% check for adding in muscle structure array
SSA = row{muscle_SSA_col};
if ~isnan(SSA)
% Assumes that all muscle data are present & valid is
% SSA is defined.
muscle_idx = muscle_idx + 1;
SSA = row{muscle_SSA_col};
SSI = row{muscle_SSI_col};
SSO = row{muscle_SSO_col};
SSD = row{muscle_SSD_col};
ISA = row{muscle_ISA_col};
ISI = row{muscle_ISI_col};
ISO = row{muscle_ISO_col};
ISD = row{muscle_ISD_col};
SCA = row{muscle_SCA_col};
SCI = row{muscle_SCI_col};
SCO = row{muscle_SCO_col};
SCD = row{muscle_SCD_col};
TMA = row{muscle_ISA_col};
TMI = row{muscle_ISI_col};
TMO = row{muscle_ISO_col};
TMD = row{muscle_ISD_col};
muscle(muscle_idx).CT_id = CT_id;
muscle(muscle_idx).SSA = SSA;
muscle(muscle_idx).SSI = SSI;
muscle(muscle_idx).SSO = SSO;
muscle(muscle_idx).SSD = SSD;
muscle(muscle_idx).ISA = ISA;
muscle(muscle_idx).ISI = ISI;
muscle(muscle_idx).ISO = ISO;
muscle(muscle_idx).ISD = ISD;
muscle(muscle_idx).SCA = SCA;
muscle(muscle_idx).SCI = SCI;
muscle(muscle_idx).SCO = SCO;
muscle(muscle_idx).SCD = SCD;
muscle(muscle_idx).TMA = TMA;
muscle(muscle_idx).TMI = TMI;
muscle(muscle_idx).TMO = TMO;
muscle(muscle_idx).TMD = TMD;
end
end
end
end
end
fprintf(' Done\n');
end
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