Merge pull request #19 from timholy/teh/no_z

Support files that are 2d vs time

src/ImagineFormat.jl

@@ -29,15 +29,12 @@ function load(io::Stream{format"Imagine"}; mode="r")
     camfilename = basename*".cam"
     Traw = h["pixel data type"]
     T = Traw <: Unsigned ? Normed{Traw, h["original image depth"]} : Traw
-    sz = [h["image width"], h["image height"], h["frames per stack"], h["nStacks"]]
-    if sz[4] == 1
-        sz = sz[1:3]
-        if sz[3] == 1
-            sz = sz[1:2]
-        end
-    end
     havez = h["frames per stack"] > 1
     havet = h["nStacks"] > 1
+    sz = havez & havet ? [h["image width"], h["image height"], h["frames per stack"], h["nStacks"]] :
+         havez ? [h["image width"], h["image height"], h["frames per stack"]] :
+         havet ? [h["image width"], h["image height"], h["nStacks"]] :
+         [h["image width"], h["image height"]]
     # Check that the file size is consistent with the expected size
     if !isfile(camfilename)
         warn("Cannot open ", camfilename)
@@ -228,7 +225,7 @@ const field_key_dict = Dict{AbstractString,Function}(
     "x translation in pixels"      => x->parse(Int,x) != 0,
     "y translation in pixels"      => x->parse(Int,x) != 0,
     "rotation angle in degree"     => x->parse(Float64,x) != 0)
- 
+
 
 function parse_header(s::IOStream)
     headerdict = Dict{String, Any}()

test/no_z.cam

@@ -0,0 +1 @@
+c��ې�Ȣ�U��U���RF4�Ez<�X��L����#�&�ڒߖf�d#���p�67�9z�>ch� ng�Ty§�}�!��p�����υ��kl;��U�����'��y���[ N��k��

test/no_z.imagine

@@ -0,0 +1,45 @@
+IMAGINE
+[general]
+header version=5.1
+app version=0.9, build (Apr 20 2007, 12:24:54)
+date and time=2007-05-09T14:46:30
+byte order=l
+
+[misc params]
+stimulus file content=
+comment=
+ai data file=G:/2007_05_09/vno_baseline.ai
+image data file=G:/2007_05_09/vno_baseline.stacks\stack_%1_
+piezo=start position: 0 um;stop position: 0 um;output scan rate: 10000
+
+[ai]
+nscans=-1
+channel list=0 1 2 3
+label list=piezo$stimuli$camera frame TTL$heartbeat
+scan rate=10000
+min sample=-2048
+max sample=2047
+min input=-10
+max input=10
+
+[camera]
+original image depth=14
+saved image depth=14
+image width=6
+image height=5
+number of frames requested=2
+nStacks=2
+idle time between stacks=3 s
+pre amp gain=3.1
+EM gain=0
+exposure time=0.05 s
+vertical shift speed=1.9176 us
+vertical clock vol amp=0
+readout rate=35 MHz
+pixel order=x y z
+frame index offset=0
+frames per stack=1
+pixel data type=uint16
+camera=DV8285_BV
+um per pixel=-1
+binning=hbin:1;vbin:1;hstart:1;hend:1004;vstart:1;vend:1002

test/runtests.jl

@@ -73,3 +73,10 @@ B[1,1,1,2] = -1.0
 @test A[1,1,4,2] == -1.0
 @test all(A[:,:,1:4,[1;3;4;5]] .== A_copy[:,:,1:4,[1;3;4;5]]) #make sure we only changed one index
 
+img = load("no_z.imagine")
+@test eltype(img) == N2f14
+@test ndims(img) == 3
+@test size(img) == (6,5,2)
+@test timedim(img) == 3
+@test axisnames(img) == (:x, :l, :time)
+@test pixelspacing(img) == (-1μm, -1μm)