Added Code and Results

Data Preparation/ORION/Modelnet/functions/binlist_to_hdf5.m

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+function binlist_to_hdf5(bins_list,h5_filename,h5_text_filename,chunk_size,run_on_cluster,write_just_this_chunk)
+%%%
+%%% In this function we assume the list is formatted as '%s %d %d %d'
+%%% where the first integer is ignored, the second is class label and the 
+%%% 3rd one is the pose_label.
+%%% We put the pose-label in the file, eventhough sometimes it's not used; It's safe -- tested!
+%%%
+
+%-- Load the list
+[files,l1,l2,l3] = textread(bins_list,'%s %d %d %d');
+N = numel(files);
+
+if(~exist('chunk_size','var')), chunk_size = 10000;end
+nchunks = ceil(N/chunk_size);
+
+%-- Create the target dir(s) if needed
+[pathstr,~,~] = fileparts(h5_filename);
+system(['wsl mkdir -p ' pathstr]);
+[pathstr,~,~] = fileparts(h5_text_filename);
+system(['wsl mkdir -p ' pathstr]);
+
+%-- See which chunks should we create
+if(exist('write_just_this_chunk','var') && any(write_just_this_chunk))
+    chunk_list = write_just_this_chunk;
+else
+    chunk_list = 1 : nchunks;
+end
+
+%--- create the text file containing names of files (only if we should!)
+if(numel(chunk_list) == nchunks)
+    create_the_text_file(h5_text_filename,h5_filename,nchunks)
+end
+
+
+%--- If we should submit jobs to cluster
+if(exist('run_on_cluster','var') && run_on_cluster)
+
+
+    for the_chunk = chunk_list
+        cmd = sprintf(['matlabD -nosplash -r "run ~/startup.m; '...
+            'binlist_to_hdf5(''%s'',''%s'',''%s'',%d,0,%d); '...
+            'exit"'],bins_list,h5_filename,h5_text_filename,chunk_size,the_chunk);
+
+	temp_job_dir= [ getenv('HOME') '/temp_cluster_job' ];
+        [~,~,wait_file{the_chunk}] = cluster_submit_job('lmbtorque',cmd,temp_job_dir,6,'6G',0,'',3,0);
+        pause(1);
+    end
+
+    return;
+end
+
+fprintf('Source: %s\nDestination1: %s\nDestination2: %s\n',bins_list,h5_filename,h5_text_filename);
+%--- Load the first bin to obtain the dimensions
+temp_v = load_binary_voxelgrid(files{1});
+d1= size(temp_v,1);
+d2= size(temp_v,2);
+d3= size(temp_v,3);
+
+
+if(~exist('write_just_this_chunk','var')), 
+    write_just_this_chunk = 0;
+end
+
+for c = chunk_list
+    fprintf('Chunk: %d/%d\n',c,nchunks);
+
+    written_sofar = (c-1)*chunk_size;
+    this_chunk_size = min(chunk_size,N-written_sofar);
+    ind1 = written_sofar+1;
+    ind2 = ind1+this_chunk_size-1;
+
+    %--- Load bins one by one and keep in memory
+    disp('Loading bin files...');
+    Data = zeros(d1,d2,d3,1,this_chunk_size);
+    tic
+    for i = 1 : this_chunk_size %I have tried parfor here previously. It makes it slower!!
+        data = load_binary_voxelgrid(files{ind1+i-1});
+        Data(:,:,:,1,i) = data;
+        if(~mod(i,50)), fprintf('%d ',i);end            
+    end
+    fprintf('\n');
+    toc
+    Data = uint8(Data);
+
+
+    %-- Write the hdf5 file(s)
+    disp('Writing the hdf5 file(s)...');
+
+    %- get the appropriate filename for this chunk
+    filename = get_chunk_filename(c,h5_filename);
+
+    if(exist(filename,'file')),delete(filename);end
+
+    h5create(filename,'/data',[d3 d2 d1 1 this_chunk_size],'Datatype','uint8');
+    h5create(filename,'/label',[1 this_chunk_size]);
+    h5create(filename,'/label_pose',[1 this_chunk_size])
+    h5write(filename,'/data',Data);
+    h5write(filename,'/label',l2(ind1:ind2)');
+    h5write(filename,'/label_pose',l3(ind1:ind2)');
+
+end
+end
+
+function filename = get_chunk_filename(chunk,h5_filename)
+   if chunk == 1
+       filename = h5_filename;
+   else
+       filename = sprintf('%s.%04d',h5_filename,chunk);
+   end
+end
+
+function create_the_text_file(textfilename,h5filename,nchunks)
+   fp = fopen(textfilename,'wt');
+   for c = 1 : nchunks
+       fprintf(fp,'%s\n',get_chunk_filename(c,h5filename));
+   end
+   fclose(fp);
+end

Data Preparation/ORION/Modelnet/functions/load_binary_voxelgrid.m

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+function v = load_binary_voxelgrid(filename)
+
+fp = fopen(filename,'rb');
+sz = fread(fp,3,'uint16');
+v = zeros(sz');
+v(:) = fread(fp,prod(sz),'uint8');
+fclose(fp);

Data Preparation/ORION/Modelnet/functions/modelnet_add_labels_to_list.m

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+function modelnet_add_labels_to_list(source_list_file,dest_list_file,rotation_start_index,Pose_file)
+
+list = textread(source_list_file,'%s');
+Pose=importdata(Pose_file,'\t');
+%parfor
+parfor i = 1 : numel(list)
+    % extracts from folder classname e.g bathtub and from the filename it
+    % extracts the index of the rotation e.g 1
+    [class_name,rotation] = modelnet_extract_classname_and_rot_from_filename(list{i});  
+    % rotation-rotation_start_index to bring rotation index in [0, maxrot-1]
+    % return the class label [0, maxclass-1] anc the pose label
+    % if all_singlerots_to_zero=1 then fo all the classes with only 1
+    % orientation it gives the the label 0 (independently from the class)
+    % otherwise it gives an increasing number based on actual orientation,
+    % class number and previus classes orientation labelling
+    [class_label,pose_label] = modelnet_generate_class_and_pose_labels(class_name,rotation-rotation_start_index,Pose);
+    list{i} = sprintf('%s %d %d %d' ,list{i},1,class_label,pose_label);
+end
+
+%--- write the modified list to the destination file
+fp = fopen(dest_list_file,'wt');
+fprintf(fp,'%s\n',list{:});
+fclose(fp);
+end
+
+
+function [class_name,rotation] = modelnet_extract_classname_and_rot_from_filename(filename)
+
+s = strsplit(filename,{'.','/'});
+class_name = s{end-4};
+r = strsplit(s{end-1},'_');
+rotation = str2double(r(end));
+end
+
+function [class_label,pose_label] = modelnet_generate_class_and_pose_labels(class_name,rotation,Pose)
+
+%%% Note: Class Label and Pose Label both start from 0.
+classes=Pose.textdata';
+nrot=Pose.data';
+
+%--- Find the Class Label
+[valid_class,class_label] = ismember(class_name,classes);
+if(~valid_class)
+    class_label = -1;
+    pose_label = -1;
+    return;
+end
+class_label = class_label - 1;     %to start from 0
+
+%--- Find the rotation label
+cr = cumsum(nrot);
+cr = circshift(cr,[0,1]);
+cr(1) = 0;
+pose_label = cr(class_label+1) + mod(rotation,nrot(class_label+1));
+
+end
+

Data Preparation/ORION/Modelnet/main.m

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+addpath(genpath('polygon2voxel/'));
+addpath(genpath('functions/'));
+
+modelnet10_classes = {'bathtub','bed','chair','desk','dresser','monitor','night_stand','sofa','table','toilet'};
+modelnet40_classes = {'airplane','bathtub','bed','bench','bookshelf','bottle','bowl','car',...
+    'chair','cone','cup','curtain','desk','door','dresser','flower_pot','glass_box',...
+    'guitar','keyboard','lamp','laptop','mantel','monitor','night_stand','person',...
+    'piano','plant','radio','range_hood','sink','sofa','stairs','stool','table',...
+    'tent','toilet','tv_stand','vase','wardrobe','xbox'};
+
+
+%-------------------- Modelnet Data Preparation ---------------
+%----------------------------------------------------------------
+%----------------------------------------------------------------
+off_path='../../datasets/ModelNet40';
+mat_path='../../datasets/ModelNet40_voxelized_mat';
+bin_path = '../../datasets/ModelNet40_bin_from_mat/';
+
+%--- convert original .off to .mat files------
+%----------------(voxel grids)----------------
+%---------------------------------------------
+volume_size = 24;
+pad_size = 3;
+angle_inc = 15;
+modelnet_off2mat(off_path,mat_path,modelnet40_classes,volume_size,pad_size,angle_inc);
+
+%---------------------------------------------
+%---------- convert .mat to .bin files -------
+%---------------------------------------------
+D = 3; %padding on each side.
+%We convert 30 to 36, such that after cropping we get 32, similar to what voxnet does
+modelnet_mat2bin(D,mat_path,bin_path, angle_inc);
+
+%---------------------------------------------
+%--------- convert bin to HDF5 chunks --------
+%---------------------------------------------
+Pose_plan='poseplan_MN40_24';
+modelnet_binlist2hdf5(bin_path,Pose_plan,angle_inc);
+%---------------------------------------------

Data Preparation/ORION/Modelnet/modelnet_binlist2hdf5.m

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+function modelnet_binlist2hdf5(DestinationFolder,Pose_plan,angle_inc)
+
+Pose_file=['../poseplans/' Pose_plan '.txt'];
+if ~exist(strcat(DestinationFolder,Pose_plan,'/'), 'dir')
+    mkdir(strcat(DestinationFolder,Pose_plan,'/'));
+end
+copyfile(Pose_file,strcat(DestinationFolder,Pose_plan,'/'));
+
+%% ---- Create the lists
+rotation_start_index = 1; %this is the original Shapenet convention
+lists_dir = sprintf('%s/%s',DestinationFolder,Pose_plan);
+alllist_file = sprintf('%s/all.txt',lists_dir);
+
+system(sprintf('wsl find %s -path "*/%s/*" -iname ''*.%s'' | wsl sort -V > %s', DestinationFolder,num2str(angle_inc),'bin',alllist_file));
+%
+modelnet_add_labels_to_list(alllist_file,alllist_file,rotation_start_index,Pose_file);
+
+% preparing training validation test lists
+for set = {'train','test','validation'}
+    dest_filename = sprintf('%s/%s.txt',lists_dir,set{1});
+    system(sprintf('wsl grep ''/%s/'' %s > %s',set{1},alllist_file,dest_filename));
+end
+
+%% --- Create some special HDF5 datasets
+binlist_to_hdf5([lists_dir '/train.txt'],[DestinationFolder '/' Pose_plan '/hdf5/train/train.hdf5'],[DestinationFolder '/' Pose_plan '/hdf5/train/train.txt'],1000);
+binlist_to_hdf5([lists_dir '/validation.txt'],[DestinationFolder '/' Pose_plan '/hdf5/validation/validation.hdf5'],[DestinationFolder '/' Pose_plan '/hdf5/validation/validation.txt'],1000);
+binlist_to_hdf5([lists_dir '/test.txt'],[DestinationFolder '/' Pose_plan '/hdf5/test/test.hdf5'],[DestinationFolder '/' Pose_plan '/hdf5/test/test.txt'],1000);

Data Preparation/ORION/Modelnet/modelnet_mat2bin.m

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+function modelnet_mat2bin(D,SourceFolder,DestinationFolder, angle_inc)
+%%% This function loads the files in the folders one by one, and saves the bin
+%%% versions to a similar subdir in the destination (tries to create it).
+%%% We go folder by folder, so that Matlab doesn't need to call the SLOW
+%%% fileparts function to find the folder names
+
+%--- Generate folders list
+temp_folders_list_file = 'temp_modelnet_folders.txt';
+disp('Generating folders list...');
+system(sprintf('wsl find %s -mindepth 3 -type d -path "*/%s/*"> %s',SourceFolder,num2str(angle_inc),temp_folders_list_file));
+
+%--- Load the folders list
+folders_list = textread(temp_folders_list_file,'%s');
+
+%--- Loop on the folders
+disp('Converting files...');
+tic;
+for d = 1 : numel(folders_list)
+    d
+    folder = folders_list{d};
+
+    %--- Make the destination subfolder
+    relative_folder = folder(length(SourceFolder)+2:end);
+    system(sprintf('wsl mkdir %s/classes/%s -p',DestinationFolder,relative_folder));
+
+    %--- Get the list of files in each folder
+    files_list = dir(sprintf('%s/*mat',folder));
+
+    %--- Loop on file names
+     parfor f = 1 : numel(files_list)
+
+        filename = [files_list(f).name];
+        fullfilename = [SourceFolder '/' relative_folder '/' filename];
+
+        %- Load the Mat file
+        v = load(fullfilename);
+        v = v.instance;
+
+        %-- padding
+        avoxel = zeros(size(v)+2*D);
+        avoxel(1+D:end-D,1+D:end-D,1+D:end-D) = v;
+        v = avoxel;
+
+        %- Generate the bin filename
+        dest_filename = [DestinationFolder '/classes/' relative_folder '/' filename(1:end-3) 'bin'];
+
+        %- Save the bin
+        fp = fopen(dest_filename,'w');
+        fwrite(fp,uint16(size(v)),'uint16');
+        fwrite(fp,uint8(v),'uint8');
+        fclose(fp);
+
+    end
+end
+
+disp('Done');
+toc
+
+

Data Preparation/ORION/Modelnet/modelnet_off2mat.m

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+function modelnet_off2mat(off_path, data_path, classes, volume_size, pad_size, angle_inc)
+% Put the mesh object in a volume grid and save the volumetric
+% represenation file.
+% This is the input volumetric data for 3D ShapeNets.
+% off_path: root off data folder
+% data_path: destination volumetric data folder
+
+phases = {'train', 'test', 'validation'};
+
+for c = 1 : length(classes)
+    fprintf('writing the %s category\n', classes{c});
+    category_path = [off_path '/' classes{c}];
+    dest_path = [data_path '/' classes{c} '/' num2str(angle_inc)];
+    if ~exist(dest_path, 'dir')
+        mkdir(dest_path);
+    end
+    % for train, test, validation phases
+    for t = 1 : numel(phases)
+        phase = phases{t};
+        off_list = [category_path '/' phase];
+        dest_tsdf_path = [dest_path '/' phase];
+        if ~exist(dest_tsdf_path, 'dir')
+            mkdir(dest_tsdf_path);
+        end
+        files = dir(off_list);
+        for i = 1 : length(files)     
+            if strcmp(files(i).name, '.') || strcmp(files(i).name, '..') || files(i).isdir == 1 || ~strcmp(files(i).name(end-2:end), 'off')
+                continue;
+            end
+
+            filename = [off_list '/' files(i).name];
+            for viewpoint = 1 : 360/angle_inc
+                destname = [dest_tsdf_path '/' files(i).name(1:end-4) '_' num2str(viewpoint) '.mat'];
+                off_data = off_loader(filename, (viewpoint-1)*angle_inc);
+                instance = polygon2voxel(off_data, [volume_size, volume_size, volume_size], 'auto');
+                instance = padarray(instance, [pad_size, pad_size, pad_size]);
+                instance = int8(instance);
+                save(destname, 'instance');
+            end
+        end
+    end
+end
+
+function offobj = off_loader(filename, theta)
+
+offobj = struct();
+fid = fopen(filename, 'rb');
+OFF_sign = fscanf(fid, '%c', 3);
+assert(strcmp(OFF_sign, 'OFF') == 1);
+
+info = fscanf(fid, '%d', 3);
+offobj.vertices = reshape(fscanf(fid, '%f', info(1)*3), 3, info(1))';
+offobj.faces = reshape(fscanf(fid, '%d', info(2)*4), 4, info(2))';
+
+% do some translation and rotation
+center = (max(offobj.vertices) + min(offobj.vertices)) / 2;
+offobj.vertices = bsxfun(@minus, offobj.vertices, center);
+
+% and rotation
+theta = theta * pi / 180;
+R = [cos(theta), -sin(theta), 0;
+     sin(theta), cos(theta) , 0;
+        0      ,    0       , 1];
+
+offobj.vertices = offobj.vertices * R;
+
+% These vertices to define faces should be offset by one to follow the matlab convention.
+offobj.faces = offobj.faces(:,2:end) + 1; 
+
+fclose(fid);