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Binary reader for Matlab #235

Merged
merged 12 commits into from
Feb 23, 2019
Merged

Binary reader for Matlab #235

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91a3a29
Minor formatting updates
donnaaboise Dec 7, 2018
d245d56
Minor formatting updates
donnaaboise Dec 7, 2018
6f489f4
Add binary reader for amrclaw
donnaaboise Dec 26, 2018
0335369
Fix warnings in syntax and usage
donnaaboise Dec 26, 2018
148f8cb
Renderer is lower case 'opengl'
donnaaboise Dec 26, 2018
c81c478
Supply default tol_lower and tol_upper
donnaaboise Dec 26, 2018
04a8df8
Fix warnings; pre-allocate amrdata
donnaaboise Dec 26, 2018
92366d3
Fix last warning
donnaaboise Dec 27, 2018
a8773d7
Check that dimensions agree
donnaaboise Dec 27, 2018
40069a3
Get rid of minor warnings Matlab complains about
donnaaboise Jan 4, 2019
34788ba
Strip ghost cells from binary data in both 2d and 3d
donnaaboise Jan 22, 2019
f061d35
More updating to formatting to get rid ofextraneous semi-colons, etc
donnaaboise Feb 2, 2019
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4 changes: 2 additions & 2 deletions src/matlab/add_patch2slice.m
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
function add_patch2slice(sdir,sval,snum,xc,yc,zc, xe,ye,ze, q,level,...
contourlevels,mappedgrid,manifold,maskflag,grid_number,blockno,...
colormapping);
colormapping)

% Internal matlab routine for Clawpack graphics.

Expand All @@ -13,7 +13,7 @@ function add_patch2slice(sdir,sval,snum,xc,yc,zc, xe,ye,ze, q,level,...
% Mask any patches that might be underneath the new patch we want to add.
if (maskflag == 1)
mask_patches(slice,sdir,level,xe(1),xe(end),ye(1),ye(end),ze(1),ze(end));
end;
end

% Get the new patch
new_patch = create_patch(xc,yc,zc,xe,ye,ze,q,sdir,sval,contourlevels,...
Expand Down
86 changes: 43 additions & 43 deletions src/matlab/create_clines.m
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Original file line number Diff line number Diff line change
Expand Up @@ -9,52 +9,52 @@
global creatingclines

if (isempty(c))
% No contour lines on this patch
h = [];
return;
end;
% No contour lines on this patch
h = [];
return;
end

st_idx = 1;
line_cnt = 0;
while (1)
cval = c(1,st_idx);
next_length = c(2,st_idx);
line_cnt = line_cnt + 1;
x_like = zeros(1,next_length) + sval;
y_like = c(1,st_idx+1:st_idx+next_length);
z_like = c(2,st_idx+1:st_idx+next_length);

[xdata,ydata,zdata] = get_xyz(x_like,y_like,z_like,sdir);

udata.cartCoords = [xdata', ydata', zdata'];
if (mappedgrid == 1 | manifold == 1)
if (mappedgrid == 1)
if (nargin('mapc2p') == 2)
[xdata,ydata] = mapc2p(xdata,ydata);
else
[xdata, ydata, zdata] = mapc2p(xdata,ydata,zdata);
end;
end;
if (manifold == 1)
creatingclines = 1; % flag for mapc2m to indicate contour lines
% are being generated: may want to shift off
% manifold slightly to avoid hidden line removal
% causing apparent gaps in contours.
set_blocknumber(blockno);
[xdata, ydata, zdata] = mapc2m(xdata,ydata);
creatingclines = 0;
end;
end;
udata.phys_vertices = [xdata', ydata', zdata'];

h(line_cnt) = line('XData',xdata,'YData',ydata,'ZData',zdata,'Color','k');
set(h(line_cnt),'Tag','on');
udata.cval = cval;
set(h(line_cnt),'UserData',udata);
st_idx = st_idx + next_length + 1;
if (st_idx > length(c))
return;
end;
end;
cval = c(1,st_idx);
next_length = c(2,st_idx);
line_cnt = line_cnt + 1;
x_like = zeros(1,next_length) + sval;
y_like = c(1,st_idx+1:st_idx+next_length);
z_like = c(2,st_idx+1:st_idx+next_length);
[xdata,ydata,zdata] = get_xyz(x_like,y_like,z_like,sdir);
udata.cartCoords = [xdata', ydata', zdata'];
if (mappedgrid == 1 || manifold == 1)
if (mappedgrid == 1)
if (nargin('mapc2p') == 2)
[xdata,ydata] = mapc2p(xdata,ydata);
else
[xdata, ydata, zdata] = mapc2p(xdata,ydata,zdata);
end
end
if (manifold == 1)
creatingclines = 1; % flag for mapc2m to indicate contour lines
% are being generated: may want to shift off
% manifold slightly to avoid hidden line removal
% causing apparent gaps in contours.
set_blocknumber(blockno);
[xdata, ydata, zdata] = mapc2m(xdata,ydata);
creatingclines = 0;
end
end
udata.phys_vertices = [xdata', ydata', zdata'];
h(line_cnt) = line('XData',xdata,'YData',ydata,'ZData',zdata,'Color','k');
set(h(line_cnt),'Tag','on');
udata.cval = cval;
set(h(line_cnt),'UserData',udata);
st_idx = st_idx + next_length + 1;
if (st_idx > length(c))
break;
end
end

set_clines(h);
48 changes: 28 additions & 20 deletions src/matlab/create_patch.m
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,8 +4,8 @@

% Internal matlab routine for Clawpack graphics.

[xe_like, ye_like, ze_like] = get_xyzlike(xe,ye,ze,sdir);
[xc_like, yc_like, zc_like] = get_xyzlike(xc,yc,zc,sdir);
[~, ye_like, ze_like] = get_xyzlike(xe,ye,ze,sdir);
[~, yc_like, zc_like] = get_xyzlike(xc,yc,zc,sdir);

% -----------x---------------------------------------
% Create patch with q data
Expand Down Expand Up @@ -49,43 +49,51 @@
[mv_names{1:3}] = get_xyzlike('mx','my','mz',sdir);
[dv_names{1:3}] = get_xyzlike('dx','dy','dz',sdir);

for i = 1:3,
userdata = setfield(userdata,(vc_names{i}),vc{i});
userdata = setfield(userdata,(ve_names{i}), ve{i});
userdata = setfield(userdata,(mv_names{i}),length(vc{i}));
for i = 1:3
% userdata = setfield(userdata,(vc_names{i}),vc{i});
% userdata = setfield(userdata,(ve_names{i}), ve{i});
% userdata = setfield(userdata,(mv_names{i}),length(vc{i}));
userdata.(vc_names{i}) = vc{i};
userdata.(ve_names{i}) = ve{i};
userdata.(mv_names{i}) = numel(vc{i});

% If we are doing a manifold, then dz==1.
dv = ve{i}(2) - ve{i}(1);
userdata = setfield(userdata,(dv_names{i}),(dv == 0) + dv*(dv ~= 0));
end;
% userdata = setfield(userdata,(dv_names{i}),(dv == 0) + dv*(dv ~= 0));
userdata.(dv_names{i}) = (dv == 0) + dv*(dv ~= 0);
end

[vmin_names{1:3}] = get_xyzlike('xmin','ymin','zmin',sdir);
[vmax_names{1:3}] = get_xyzlike('xmax','ymax','zmax',sdir);
userdata = setfield(userdata,vmin_names{1},sval);
userdata = setfield(userdata,vmax_names{1},sval);
for i = 2:3,
userdata = setfield(userdata,(vmin_names{i}), ve{i}(1));
userdata = setfield(userdata,(vmax_names{i}), ve{i}(end));
end;
% userdata = setfield(userdata,vmin_names{1},sval);
% userdata = setfield(userdata,vmax_names{1},sval);
userdata.(vmin_names{1}) = sval;
userdata.(vmax_names{1}) = sval;
for i = 2:3
%userdata = setfield(userdata,(vmin_names{i}), ve{i}(1));
%userdata = setfield(userdata,(vmax_names{i}), ve{i}(end));
userdata.(vmin_names{i}) = ve{i}(1);
userdata.(vmax_names{i}) = ve{i}(end);
end

% Store Cartesian coodinates for use in mask_patches, and convert patch
% vertices to physical coordinates.
v = get(p,'Vertices');
userdata.cartCoords = v;

if (mappedgrid == 1 | manifold == 1)
if (mappedgrid == 1 || manifold == 1)
if (mappedgrid == 1)
if (nargin('mapc2p') == 2)
[v(:,1),v(:,2)] = mapc2p(v(:,1),v(:,2));
else
[v(:,1),v(:,2),v(:,3)] = mapc2p(v(:,1),v(:,2),v(:,3));
end;
end;
end
end
if (manifold == 1)
[v(:,1),v(:,2), v(:,3)] = mapc2m(v(:,1),v(:,2));
end;
end
set(p,'Vertices',v);
end;
end
userdata.phys_vertices = v;

% -------------------------------------------------------
Expand All @@ -97,7 +105,7 @@
if (~isempty(contourlevels))
c = contourc(yc_like,zc_like,qcm2,contourlevels);
userdata.contourLines = create_clines(c,sval,sdir,mappedgrid,manifold,blockno);
end;
end

% Mesh data for showing coarsened mesh later...
% userdata.mesh = create_mesh(sdir,sval,xe,ye,ze,mappedgrid,manifold);
Expand Down
175 changes: 98 additions & 77 deletions src/matlab/create_sliceintersections.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,80 +7,101 @@ function create_sliceintersections(mappedgrid)
ve_names = {'xe','ye','ze'};
isect_names = {'yzIntersect','xzIntersect','xyIntersect'};

for idir = 1:3,
for jdir = (idir+1):3,
slices_idir = get_slices(sdirs{idir});
slices_jdir = get_slices(sdirs{jdir});

% Now consider all pair-wise combinations of these two sets of slices
for n = 1:length(slices_idir);
for m = 1:length(slices_jdir);

% cell2mat doesn't seem to exist on some versions of Matlab
% so I have copied my matlab version to ../matlab2 files.
% pvec = cell2mat_claw(slices_idir{n});
% qvec = cell2mat_claw(slices_jdir{m});

pvec = [];
qvec = [];
% Need a big list of all patches we can intersect
for ll = 1:length(slices_idir{n}),
pvec = [pvec slices_idir{n}{ll}];
end;

for ll = 1:length(slices_jdir{m}),
qvec = [qvec slices_jdir{m}{ll}];
end;

for k = 1:length(pvec),
for l = 1:length(qvec),
p = pvec(k);
q = qvec(l);

udata_p = get(p,'UserData');
udata_q = get(q,'UserData');

np = udata_p.grid_number;
nq = udata_q.grid_number;
if (np == nq)
% This sets two of the coordinates for the line we are going
% to draw
sval_p = udata_p.sval;
sval_q = udata_q.sval;

kdir = (1:3);
kdir([idir; jdir]) = [];

% Third direction is all that is left
ke = getfield(udata_p,ve_names{kdir});
vdata{idir} = sval_p + 0*ke;
vdata{jdir} = sval_q + 0*ke;
vdata{kdir} = ke;

if (mappedgrid == 1)
[xdata, ydata, zdata] = mapc2p(vdata{:});
else
[xdata, ydata, zdata] = deal(vdata{:});
end;

h = line('XData',xdata, 'YData',ydata,'ZData',zdata);

sp = getfield(udata_p,isect_names{kdir});
sp(end+1).line = h;
sp(end+1).sharedPatch = q;

sq = getfield(udata_q,isect_names{kdir});
sq(end+1).line = h;
sq(end+1).sharedPatch = p;

udata_p = setfield(udata_p,isect_names{kdir},sp);
udata_q = setfield(udata_q,isect_names{kdir},sq);
set(p,'UserData',udata_p);
set(q,'UserData',udata_q);
end; % np == nq
end; % (l) loop over all patches
end; % (k) loop over all patches
end; % (m) loop over all slices
end; % (n) loop over all slices
end; % jdir
end; % idir
vdata = cell(3,1);

for idir = 1:3
for jdir = (idir+1):3
slices_idir = get_slices(sdirs{idir});
slices_jdir = get_slices(sdirs{jdir});

% Now consider all pair-wise combinations of these two sets of slices
for n = 1:length(slices_idir)
for m = 1:length(slices_jdir)

l1 = 0;
for ll = 1:length(slices_idir{n})
l1 = l1 + numel(slices_idir{n}{ll});
end

pvec = zeros(l1,1);
% Need a big list of all patches we can intersect
k = 1;
for ll = 1:length(slices_idir{n})
ps = slices_idir{n}{ll};
for jj = 1:length(ps)
pvec(k) = ps(jj);
k = k + 1;
end
end

l2 = 0;
for ll = 1:length(slices_jdir{m})
l2 = l2 + numel(slices_jdir{m}{ll});
end

qvec = zeros(l2,1);
% Need a big list of all patches we can intersect
k = 1;
for ll = 1:length(slices_jdir{m})
ps = slices_jdir{m}{ll};
for jj = 1:length(ps)
qvec(k) = ps(jj);
k = k + 1;
end
end

for k = 1:length(pvec)
for l = 1:length(qvec)
p = pvec(k);
q = qvec(l);

udata_p = get(p,'UserData');
udata_q = get(q,'UserData');

np = udata_p.grid_number;
nq = udata_q.grid_number;
if (np == nq)
% This sets two of the coordinates for the line we are going
% to draw
sval_p = udata_p.sval;
sval_q = udata_q.sval;

kdir = (1:3);
kdir([idir; jdir]) = [];

% Third direction is all that is left
% ke = getfield(udata_p,ve_names{kdir});
ke = udata_p.(ve_names{kdir});
vdata{idir} = sval_p + 0*ke;
vdata{jdir} = sval_q + 0*ke;
vdata{kdir} = ke;

if (mappedgrid == 1)
[xdata, ydata, zdata] = mapc2p(vdata{:});
else
[xdata, ydata, zdata] = deal(vdata{:});
end

h = line('XData',xdata, 'YData',ydata,'ZData',zdata);

% sp = getfield(udata_p,isect_names{kdir});
sp = udata_p.(isect_names{kdir});
sp(end+1).line = h;
sp(end+1).sharedPatch = q;

%sq = getfield(udata_q,isect_names{kdir});
sq = udata_q.(isect_names{kdir});
sq(end+1).line = h;
sq(end+1).sharedPatch = p;

udata_p.(isect_names{kdir}) = sp;
udata_q.(isect_names{kdir}) = sq;
set(p,'UserData',udata_p);
set(q,'UserData',udata_q);
end % np == nq
end % (l) loop over all patches
end % (k) loop over all patches
end % (m) loop over all slices
end % (n) loop over all slices
end % jdir
end % idir
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