-
Notifications
You must be signed in to change notification settings - Fork 7
/
cajal3d.m
254 lines (213 loc) · 10.3 KB
/
cajal3d.m
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
classdef cajal3d
%% cajal3d - CAJAL3D Framework utility Class
% This function is provided to perform basic configuration, help, and
% bug reporting tasks.
%
% Supported Uses:
%
% Add framework to MATALB search path and setup:
% >> cajal3d
% - or -
% >> cajal3d.setSearchPath
%
% Note: If you have not set your MATLAB installation to automatically
% add the CAJAL3D framework to the search path at startup either
% manually, or using the 'setupEnvironment' script, you must run this
% everytime MATLAB start before you can use the CAJAL3D framework.
%
% Set the current MATLAB folder to the framework path:
% >> cajal3d.setCurrentFolder
%
% Get the framework path:
% >> cajal3d.getRootDir
%
% Install a CAJAL3D toolbox where toolbox_path = path to startup script
% for the toolbox you wish to add.
% >> cajal3d.installToolbox(toolbox_path)
%
% List installed toolboxes:
% >> cajal3d.listInstalledToolboxes()
%
% Remove an installed toolbox:
% >> cajal3d.uninstallToolbox()
%
% Print information to be included in a bug report:
% >> cajal3d.bugReport
%
% Note: Run this command immediately after the error has occured!
%
% Get the framework version:
% >> cajal3d.version
%
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Copyright 2015 The Johns Hopkins University / Applied Physics Laboratory
% All Rights Reserved.
% Contact the JHU/APL Office of Technology Transfer for any additional rights.
% www.jhuapl.edu/ott
%
% Licensed under the Apache License, Version 2.0 (the "License");
% you may not use this file except in compliance with the License.
% You may obtain a copy of the License at
%
% http://www.apache.org/licenses/LICENSE-2.0
%
% Unless required by applicable law or agreed to in writing, software
% distributed under the License is distributed on an "AS IS" BASIS,
% WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
% See the License for the specific language governing permissions and
% limitations under the License.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
properties(SetAccess = 'private', GetAccess = 'public')
frameworkRoot = '';
end
properties(Constant = true)
version = '1.7';
POC = '[email protected]';
end
methods
function this = cajal3d
% set up search path on constructor
pathstr = cajal3d.setSearchPath;
this.frameworkRoot = pathstr;
% set up any installed CAJAL3D toolboxes
if exist(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'),'file')
load(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'));
for ii = 1:length(toolbox_setup) %#ok<USENS>
run(toolbox_setup{ii});
end
end
% set up dynamic class path
javaaddpath(fullfile(cajal3d.getRootDir,'api','matlab','ocp','jedis-2.1.0.jar'));
javaaddpath(fullfile(cajal3d.getRootDir,'api','matlab','ocp','cajal3d.jar'));
warning('off','MATLAB:Java:DuplicateClass');
end
end
methods (Static)
function bugReport
err = lasterror; %#ok<LERR>
clc
bugStr = sprintf('* Please copy and paste the following report into an email addressed to <a href="mailto:%s?subject=CAJAL3D_Bug_Report">%s</a> *\n',...
cajal3d.POC,cajal3d.POC);
bugStr = sprintf('%s* In addition to your contact information, feel free to include *\n* any additional comments and/or attachments that may help debug the issue. *\n\n',bugStr);
bugStr = sprintf('%s\n<><><><><> BUG REPORT <><><><><>\n\n',bugStr);
bugStr = sprintf('%sUserpath Env Var: %s\n\n',bugStr,getenv('MATLAB_USE_USERPATH'));
bugStr = sprintf('%sArch: %s\n\n',bugStr,computer('arch'));
bugStr = sprintf('%sOS String: %s\n\n',bugStr,system_dependent('getos'));
if ispc
platform = [system_dependent('getos'),' ',system_dependent('getwinsys')];
elseif ismac
[fail, input] = unix('sw_vers');
if ~fail
platform = strrep(input, 'ProductName:', '');
platform = strrep(platform, sprintf('\t'), '');
platform = strrep(platform, sprintf('\n'), ' ');
platform = strrep(platform, 'ProductVersion:', ' Version: ');
platform = strrep(platform, 'BuildVersion:', 'Build: ');
else
platform = system_dependent('getos');
end
else
platform = system_dependent('getos');
end
% display version
bugStr = sprintf('%sMATLAB Version: %s\n',bugStr,version);
% display Matlab license number
bugStr = sprintf('%sMATLAB License Number: %s\n',bugStr,license);
% display os
bugStr = sprintf('%sOperating System: %s\n',bugStr,platform);
% display first line of Java VM version info
bugStr = sprintf('%sJava VM Version: %s\n',bugStr,...
char(strread(version('-java'),'%s',1,'delimiter','\n')));
% toolbox info
bugStr = sprintf('%s\nToolboxes: \n',bugStr);
v = ver;
for k=1:length(v)
bugStr = sprintf('%s %s - Version %s\n', ...
bugStr,v(k).Name, v(k).Version);
end
% system info
bugStr = sprintf('%s\nCPU: %s\n',bugStr,system_dependent('GetCPU'));
bugStr = sprintf('%sNum Cores: %d\n',bugStr,system_dependent('NumCores'));
bugStr = sprintf('%sNum Threads: %d\n',bugStr,system_dependent('NumThreads'));
% pwd
bugStr = sprintf('%s\nCurrent Working Directory: %s\n',bugStr,pwd);
[pathstr, ~, ~] = fileparts(which('cajal3d'));
bugStr = sprintf('%sFramework Directory: %s\n\n',bugStr,pathstr);
bugStr = sprintf('%sFramework Version: %s\n\n',bugStr,cajal3d.version);
% error info
errStr = sprintf('Last Error:\n');
errStr = sprintf('%s Identifier: %s\n',errStr,err.identifier);
errStr = sprintf('%s Message: %s\n',errStr,err.message);
errStr = sprintf('%s Cause:\n',errStr);
s = err.stack;
errStr = sprintf('%s Stack:\n',errStr);
for ii = 1:length(s)
fstr = strrep(s(ii).file,'\','\\');
errStr = sprintf('%s\n File: %s \n',errStr,fstr);
errStr = sprintf('%s Method: %s \n',errStr,s(ii).name);
errStr = sprintf('%s Line: %d \n',errStr,s(ii).line);
end
bugStr = sprintf('%s%s\n\n',bugStr,errStr);
bugStr = sprintf('%sDescription of Problem: \n\n',bugStr);
bugStr = sprintf('%s - - Please fill out in email - - \n\n',bugStr);
bugStr = sprintf('%sComments: \n\n',bugStr);
bugStr = sprintf('%s - - Please fill out in email - - \n\n',bugStr);
bugStr = sprintf('%s\nPlease copy and paste the above report into an email addressed to <a href="mailto:%s?subject=CAJAL3D_Bug_Report">%s</a>.\n\n\n',...
bugStr,cajal3d.POC,cajal3d.POC);
fprintf('%s',bugStr);
end
function pathstr = setSearchPath
[pathstr, ~, ~] = fileparts(which('cajal3d'));
new_path = genpath(pathstr);
addpath(new_path);
end
function setCurrentFolder
[pathstr, ~, ~] = fileparts(which('cajal3d'));
cd(pathstr);
end
function path = getRootDir
[path, ~, ~] = fileparts(which('cajal3d'));
end
function installToolbox(path)
% This method "installs" a CAJAL3D toolbox by saving the
% provided path to its setup method. This will be run
% when "cajal3d" gets called either at the command prompt
% or automatically in startup.m
if exist(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'),'file')
load(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'));
toolbox_setup(length(toolbox_setup)+1) = {path}; %#ok<NODEF,NASGU>
else
toolbox_setup = {path}; %#ok<NASGU>
end
save(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'),'toolbox_setup');
end
function uninstallToolbox()
count = cajal3d.listInstalledToolboxes();
if count ~=0
question = sprintf('Which toolbox should be removed? [1-%d]\n',count);
resp = input(question);
load(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'));
toolbox_setup(resp) = [];
if ~isempty(toolbox_setup)
save(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'),'toolbox_setup');
else
delete(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'));
end
end
end
function count = listInstalledToolboxes()
if exist(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'),'file')
load(fullfile(cajal3d.getRootDir(),'cajal3d_toolboxes.mat'));
count = length(toolbox_setup); %#ok<USENS>
fprintf('Installed CAJAL3D toolbox startup methods:\n');
for ii = 1:length(toolbox_setup)
fprintf('[%d] %s\n',ii,toolbox_setup{ii});
end
else
fprintf('No CAJAL3D toolboxes installed.\n');
count = 0;
end
end
end
end