Reading h5 file
I am a new python user and I want to read the data from a h5 file. The code that I have used to read the data is given below:
>>> import numpy as np
>>> import h5py
>>> f = h5py.File('file.h5', 'r')
>>> list(f.keys())
[u'data']
>>> dset = f[u'data']
>>> dset.shape
(64, 64, 64)
>>> dset.dtype
dtype(('<f8', (3,)))
Can anyone help me to understand these commands? My questions are:
1. What can I understand by the terms [u'data'] and dtype(('
python-3.x numpy h5py
edited Nov 21 '18 at 3:10
hpaulj
110k774140
asked Nov 21 '18 at 1:52
Photon
31
add a comment |
I am a new python user and I want to read the data from a h5 file. The code that I have used to read the data is given below:
>>> import numpy as np
>>> import h5py
>>> f = h5py.File('file.h5', 'r')
>>> list(f.keys())
[u'data']
>>> dset = f[u'data']
>>> dset.shape
(64, 64, 64)
>>> dset.dtype
dtype(('<f8', (3,)))
Can anyone help me to understand these commands? My questions are:
1. What can I understand by the terms [u'data'] and dtype(('
python-3.x numpy h5py
edited Nov 21 '18 at 3:10
hpaulj
110k774140
asked Nov 21 '18 at 1:52
Photon
31
Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
If you are new to Python it's hard to know where there are gaps in your knowledge. To me theh5pydocs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the otherh5pytagged questions. Beyond that you need to some basic knowledge ofnumpyalong withpython.
– hpaulj
Nov 21 '18 at 3:08
add a comment |
I am a new python user and I want to read the data from a h5 file. The code that I have used to read the data is given below:
>>> import numpy as np
>>> import h5py
>>> f = h5py.File('file.h5', 'r')
>>> list(f.keys())
[u'data']
>>> dset = f[u'data']
>>> dset.shape
(64, 64, 64)
>>> dset.dtype
dtype(('<f8', (3,)))
Can anyone help me to understand these commands? My questions are:
1. What can I understand by the terms [u'data'] and dtype(('
python-3.x numpy h5py
edited Nov 21 '18 at 3:10
hpaulj
110k774140
asked Nov 21 '18 at 1:52
Photon
31
I am a new python user and I want to read the data from a h5 file. The code that I have used to read the data is given below:
>>> import numpy as np
>>> import h5py
>>> f = h5py.File('file.h5', 'r')
>>> list(f.keys())
[u'data']
>>> dset = f[u'data']
>>> dset.shape
(64, 64, 64)
>>> dset.dtype
dtype(('<f8', (3,)))
Can anyone help me to understand these commands? My questions are:
1. What can I understand by the terms [u'data'] and dtype(('
python-3.x numpy h5py
python-3.x numpy h5py
edited Nov 21 '18 at 3:10
hpaulj
110k774140
asked Nov 21 '18 at 1:52
Photon
31
edited Nov 21 '18 at 3:10
hpaulj
110k774140
asked Nov 21 '18 at 1:52
Photon
31
edited Nov 21 '18 at 3:10
hpaulj
110k774140
edited Nov 21 '18 at 3:10
hpaulj
110k774140
edited Nov 21 '18 at 3:10
hpaulj
110k774140
110k774140
asked Nov 21 '18 at 1:52
Photon
31
asked Nov 21 '18 at 1:52
Photon
31
asked Nov 21 '18 at 1:52
Photon
31
31
Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
If you are new to Python it's hard to know where there are gaps in your knowledge. To me theh5pydocs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the otherh5pytagged questions. Beyond that you need to some basic knowledge ofnumpyalong withpython.
– hpaulj
Nov 21 '18 at 3:08
add a comment |
Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
If you are new to Python it's hard to know where there are gaps in your knowledge. To me theh5pydocs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the otherh5pytagged questions. Beyond that you need to some basic knowledge ofnumpyalong withpython.
– hpaulj
Nov 21 '18 at 3:08
Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
If you are new to Python it's hard to know where there are gaps in your knowledge. To me the
h5py docs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the other h5py tagged questions. Beyond that you need to some basic knowledge of numpy along with python.– hpaulj
Nov 21 '18 at 3:08
If you are new to Python it's hard to know where there are gaps in your knowledge. To me the
h5py docs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the other h5py tagged questions. Beyond that you need to some basic knowledge of numpy along with python.– hpaulj
Nov 21 '18 at 3:08
add a comment |
1 Answer
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As @hpaulj mentions, the h5py doc is a good reference. You also need to understand basic HDF5 file concepts. It's a big topic. To get started, review the Learning HDF5 pages from The HDF Group. I know (from personal experience) that you will struggle if you don't understand how to navigate the hierarchy. Learn the differences between Group and Dataset objects.
Here's an explanation of the output in your OP.
Note that these are all h5py functions (not numpy).
>>> list(f.keys())
[u'data']
The “keys” are the names of group members, and the “values” are the members (Group and Dataset objects). This is a list of the Node names at the root level of the file. Nodes can be Groups or Datasets. In your case, you have one dataset named data. (The only group in this HDF5 file is the root group: '/', there are no groups below the root.)
The next step accesses the data in the data dataset.
>>> dset = f[u'data']
The shape attribute gives you the dimensions of the dataset:
>>> dset.shape
(64, 64, 64)
The dtype attribute gives you the data types of the dataset (just like numpy):
>>> dset.dtype
type(('<f8', (3,)))
So, you have an array of floats. If you want to see the data, you can enter this (I would only do this for small datasets, or slice to print a few rows):
>>> for row in dset:
print (row)
From here, what you do with the data is up to you.
answered Nov 21 '18 at 15:08
kcw78
308110
add a comment |
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As @hpaulj mentions, the h5py doc is a good reference. You also need to understand basic HDF5 file concepts. It's a big topic. To get started, review the Learning HDF5 pages from The HDF Group. I know (from personal experience) that you will struggle if you don't understand how to navigate the hierarchy. Learn the differences between Group and Dataset objects.
Here's an explanation of the output in your OP.
Note that these are all h5py functions (not numpy).
>>> list(f.keys())
[u'data']
The “keys” are the names of group members, and the “values” are the members (Group and Dataset objects). This is a list of the Node names at the root level of the file. Nodes can be Groups or Datasets. In your case, you have one dataset named data. (The only group in this HDF5 file is the root group: '/', there are no groups below the root.)
The next step accesses the data in the data dataset.
>>> dset = f[u'data']
The shape attribute gives you the dimensions of the dataset:
>>> dset.shape
(64, 64, 64)
The dtype attribute gives you the data types of the dataset (just like numpy):
>>> dset.dtype
type(('<f8', (3,)))
So, you have an array of floats. If you want to see the data, you can enter this (I would only do this for small datasets, or slice to print a few rows):
>>> for row in dset:
print (row)
From here, what you do with the data is up to you.
answered Nov 21 '18 at 15:08
kcw78
308110
add a comment |
As @hpaulj mentions, the h5py doc is a good reference. You also need to understand basic HDF5 file concepts. It's a big topic. To get started, review the Learning HDF5 pages from The HDF Group. I know (from personal experience) that you will struggle if you don't understand how to navigate the hierarchy. Learn the differences between Group and Dataset objects.
Here's an explanation of the output in your OP.
Note that these are all h5py functions (not numpy).
>>> list(f.keys())
[u'data']
The “keys” are the names of group members, and the “values” are the members (Group and Dataset objects). This is a list of the Node names at the root level of the file. Nodes can be Groups or Datasets. In your case, you have one dataset named data. (The only group in this HDF5 file is the root group: '/', there are no groups below the root.)
The next step accesses the data in the data dataset.
>>> dset = f[u'data']
The shape attribute gives you the dimensions of the dataset:
>>> dset.shape
(64, 64, 64)
The dtype attribute gives you the data types of the dataset (just like numpy):
>>> dset.dtype
type(('<f8', (3,)))
So, you have an array of floats. If you want to see the data, you can enter this (I would only do this for small datasets, or slice to print a few rows):
>>> for row in dset:
print (row)
From here, what you do with the data is up to you.
answered Nov 21 '18 at 15:08
kcw78
308110
add a comment |
As @hpaulj mentions, the h5py doc is a good reference. You also need to understand basic HDF5 file concepts. It's a big topic. To get started, review the Learning HDF5 pages from The HDF Group. I know (from personal experience) that you will struggle if you don't understand how to navigate the hierarchy. Learn the differences between Group and Dataset objects.
Here's an explanation of the output in your OP.
Note that these are all h5py functions (not numpy).
>>> list(f.keys())
[u'data']
The “keys” are the names of group members, and the “values” are the members (Group and Dataset objects). This is a list of the Node names at the root level of the file. Nodes can be Groups or Datasets. In your case, you have one dataset named data. (The only group in this HDF5 file is the root group: '/', there are no groups below the root.)
The next step accesses the data in the data dataset.
>>> dset = f[u'data']
The shape attribute gives you the dimensions of the dataset:
>>> dset.shape
(64, 64, 64)
The dtype attribute gives you the data types of the dataset (just like numpy):
>>> dset.dtype
type(('<f8', (3,)))
So, you have an array of floats. If you want to see the data, you can enter this (I would only do this for small datasets, or slice to print a few rows):
>>> for row in dset:
print (row)
From here, what you do with the data is up to you.
answered Nov 21 '18 at 15:08
kcw78
308110
As @hpaulj mentions, the h5py doc is a good reference. You also need to understand basic HDF5 file concepts. It's a big topic. To get started, review the Learning HDF5 pages from The HDF Group. I know (from personal experience) that you will struggle if you don't understand how to navigate the hierarchy. Learn the differences between Group and Dataset objects.
Here's an explanation of the output in your OP.
Note that these are all h5py functions (not numpy).
>>> list(f.keys())
[u'data']
The “keys” are the names of group members, and the “values” are the members (Group and Dataset objects). This is a list of the Node names at the root level of the file. Nodes can be Groups or Datasets. In your case, you have one dataset named data. (The only group in this HDF5 file is the root group: '/', there are no groups below the root.)
The next step accesses the data in the data dataset.
>>> dset = f[u'data']
The shape attribute gives you the dimensions of the dataset:
>>> dset.shape
(64, 64, 64)
The dtype attribute gives you the data types of the dataset (just like numpy):
>>> dset.dtype
type(('<f8', (3,)))
So, you have an array of floats. If you want to see the data, you can enter this (I would only do this for small datasets, or slice to print a few rows):
>>> for row in dset:
print (row)
From here, what you do with the data is up to you.
answered Nov 21 '18 at 15:08
kcw78
308110
edited Nov 21 '18 at 19:22
answered Nov 21 '18 at 15:08
kcw78
308110
answered Nov 21 '18 at 15:08
kcw78
308110
answered Nov 21 '18 at 15:08
kcw78
308110
308110
add a comment |
add a comment |
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Don't know why I can't view the full post...the missing points are given below: Can anyone help me to understand these commands? My questions are: 1. What can I understand by the terms [u'data'] and dtype(('<f8', (3,)))? 2. If I want to view the full data shape (e.g, 64,64,64) then what command I need to use in python script? 3. What is the difference between the commands, 'dset[0:63]' ,'dset[0,63]' and 'dset[0:63, 0:63]'?
– Photon
Nov 21 '18 at 1:57
If you are new to Python it's hard to know where there are gaps in your knowledge. To me the
h5pydocs are clear enough. docs.h5py.org/en/latest/high/dataset.html#reading-writing-data. I'd suggest also looking at some of the otherh5pytagged questions. Beyond that you need to some basic knowledge ofnumpyalong withpython.– hpaulj
Nov 21 '18 at 3:08