Import hdf5 file into Matlab

Hi, I am trying to use Matlab to import an hdf5 file. I am wondering if someone can help me figure out how to import the data. I attached the hdf5 file.

I used

h5info('L_600_3_Fine.0005.hdf5')

Output:

   ans = 

        Filename: 'C:\Personal\Study software\Dropbox\Software\Matlab application\Confocal depth corre...'
            Name: '/'
          Groups: [1x1 struct]
        Datasets: []
       Datatypes: []
           Links: []
      Attributes: []

It looks empty, but when I use h5disp:

h5disp('L_600_3_Fine.0005.hdf5')

Output:

HDF5 L_600_3_Fine.0005.hdf5 
Group '/' 
    Group '/2D Scan' 
        Attributes:
            'VERSION':  2.000000
            'TAG':  'S20'
            'Header':  '# 2-D Scan File created by LabVIEW Control Panel  6/9/2015 1:44:57 AM; Scan time 0 hrs 22 min 14 sec

#

# Beamline 20 ID

#

# User Comment:

#

#

# Amplifer Sensitivities:

# PreKB_I0: 10 nA/V  I0: 5 nA/V  IT: 1 nA/V  CaliDiode: 200 pA/V  

#

# Analog Input Voltages at start/end of scan:

# Preslit: 3.201/3.105  PreKB_I0: 0.229/0.120  I0: 0.100/-0.003  IT: 0.363/0.335  CaliDiode: 0.490/0.285  

#

# XIA Filters:

# 1X: OUT 2X: OUT 4X: OUT 8X: OUT

#

# Filters on XIA Shutter Unit:

# 1X: OUT 2X: OUT

#

# Mono Info:

# Angle: 9.0304 degrees; Energy from motor record: 12599.997 eV; Energy from encoder: 4503.476 eV; 2nd Xtal: 111.5 mm

#

# ID Info:

# Gap Energy: 12750.0 eV; Offset: 150.0 eV; Harmonic: 1

#

# Slit Info:

# ID I0 slits:  Center is at 250 (H), 0 (V)   Size is 1000 wide x 4000 high

# IDB slits:  Center is at 98 (H), -590 (V)   Size is 680 wide x 880 high

# KB Slits:  Center is at 0 (H), 450 (V)   Size is 200 wide x 200 high

#

# Motor Positions:

# AeroTechH (20id:m61): -12788.033000 AeroTechV (20id:m62): 14909.005000 Fine-focus-Z (20id:m51): 100.512821 ADC KB focus (20id:m54): -700.000000 

#

# Detector Names/PVs:

# Preslit/N/A  PreKB_I0/N/A  I0/N/A  IT/N/A  CaliDiode/N/A  

# ICR Ch 1/N/A  PKa_Sum/N/A  SKa_Sum/N/A  ClKa_Sum/N/A  KKa_Sum/N/A  

# CaKa_Sum/N/A  TiKa_Sum/N/A  MnKa_Sum/N/A  FeKa_Sum/N/A  NiKa_Sum/N/A  

# CuKa_Sum/N/A  ZnKa_Sum/N/A  HgLa1_Sum/N/A  AsKa_Sum/N/A  SeKa_Sum/N/A  

# Scatter_Sum/N/A  

#

# X Positioner names/Drive PVs/Readback PVs:

# XPOS AeroTechH/20id:m61.VAL/20id:m61.RBV  

#

# Y Positioner names/Drive PVs/Readback PVs:

# YPOS Fine-focus-Z/20id:m51.VAL/20id:m51.RBV  

# Here is a readable list of column headings:

#  1) AeroTechH            11) ClKa_Sum             21) AsKa_Sum             

#  2) Fine-focus-Z         12) KKa_Sum              22) SeKa_Sum             

#  3) Preslit              13) CaKa_Sum             23) Scatter_Sum          

#  4) PreKB_I0             14) TiKa_Sum             

#  5) I0                   15) MnKa_Sum             

#  6) IT                   16) FeKa_Sum             

#  7) CaliDiode            17) NiKa_Sum             

#  8) ICR Ch 1             18) CuKa_Sum             

#  9) PKa_Sum              19) ZnKa_Sum             

# 10) SKa_Sum              20) HgLa1_Sum            

#

# Column Headings:

#AeroTechH            Fine-focus-Z         Preslit              PreKB_I0             I0                   IT                   CaliDiode            ICR Ch 1             PKa_Sum              SKa_Sum              ClKa_Sum             KKa_Sum              CaKa_Sum             TiKa_Sum             MnKa_Sum             FeKa_Sum             NiKa_Sum             CuKa_Sum             ZnKa_Sum             HgLa1_Sum            AsKa_Sum             SeKa_Sum             Scatter_Sum          

'
        Dataset 'Detectors' 
            Size:  21x81x51
            MaxSize:  InfxInfxInf
            Datatype:   H5T_IEEE_F32BE (single)
            ChunkSize:  21x81x1
            Filters:  none
            FillValue:  0.000000
            Attributes:
                'Detector Names':  'Preslit', 'PreKB_I0', 'I0', 'IT', 'CaliDiode', 'ICR Ch 1', 'PKa_Sum', 'SKa_Sum', 'ClKa_Sum', 'KKa_Sum', 'CaKa_Sum', 'TiKa_Sum', 'MnKa_Sum', 'FeKa_Sum', 'NiKa_Sum', 'CuKa_Sum', 'ZnKa_Sum', 'HgLa1_Sum', 'AsKa_Sum', 'SeKa_Sum', 'Scatter_Sum'
                'DATASET_TYPE':  'DETECTORS'
        Dataset 'MCA 1' 
            Size:  1024x81x51
            MaxSize:  InfxInfxInf
            Datatype:   H5T_STD_U16BE (uint16)
            ChunkSize:  1024x81x1
            Filters:  none
            FillValue:  0
            Attributes:
                'DATASET_TYPE':  'MCA'
        Dataset 'X Positions' 
            Size:  1x81x51
            MaxSize:  InfxInfxInf
            Datatype:   H5T_IEEE_F32BE (single)
            ChunkSize:  1x81x51
            Filters:  none
            FillValue:  0.000000
            Attributes:
                'Motor Info':  'AeroTechH', '20id:m61'
                'DATASET_TYPE':  'X'
        Dataset 'Y Positions' 
            Size:  51x1
            MaxSize:  51x1
            Datatype:   H5T_IEEE_F32BE (single)
            ChunkSize:  []
            Filters:  none
            FillValue:  0.000000
            Attributes:
                'DATASET_TYPE':  'Y'
                'Motor Info':  'Fine-focus-Z', '20id:m51'

When I use HDFView to see the hdf5 file. I can see the data:

Please help me,

Thanks,

Peng

[per isakson]

Did you read

• High-Level Functions, Easily view, read, and write HDF5 files
• Importing HDF5 Files

[Peng]

Yes, I read them several times, but I still didn't find a clue. High-Level Functions, Easily view, read, and write HDF5 files Importing HDF5 Files

Answer 1

[per isakson]

I recommend

• Run some of the examples, which comes with the Matlab documentation.
• Use HDFView to explore the structure of the data file. I prefer it to h5disp.

Here is a simple example with your file.

data = h5read( 'c:\m\cssm\L_600_3_Fine.0005\L_600_3_Fine.0005.hdf5' ...
             , '/2D Scan/Detectors' );
>> whos
  Name       Size                Bytes  Class                Attributes
  data      21x81x51            347004  single

[Peng]

I really appreciate your help. I can read all the data now!