Unable to open a dataset in h5py
When I try to import a folder with h5py, I am able to open. However, when I try to access its datasets, it says there is an error. Is there a reason why?
The code below is used to import the folder:
hf = h5py.File('filename', 'r')
However, when I use the code below, there is an error:
x = np.array(hf["dataset"])
h5py hdf
asked Nov 24 '18 at 4:21
kdfkdf
61
add a comment |
When I try to import a folder with h5py, I am able to open. However, when I try to access its datasets, it says there is an error. Is there a reason why?
The code below is used to import the folder:
hf = h5py.File('filename', 'r')
However, when I use the code below, there is an error:
x = np.array(hf["dataset"])
h5py hdf
asked Nov 24 '18 at 4:21
kdfkdf
61
You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's adatasetcalleddataset? Or is that just a guess or random choice? How much of theh5py"getting started" documentation have you read (and understood)?
– hpaulj
Nov 24 '18 at 4:34
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest firstds = hf["dataset"]to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation,x = ds[:]is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use adumpscript to learn more.
– hpaulj
Nov 24 '18 at 5:25
add a comment |
When I try to import a folder with h5py, I am able to open. However, when I try to access its datasets, it says there is an error. Is there a reason why?
The code below is used to import the folder:
hf = h5py.File('filename', 'r')
However, when I use the code below, there is an error:
x = np.array(hf["dataset"])
h5py hdf
asked Nov 24 '18 at 4:21
kdfkdf
61
When I try to import a folder with h5py, I am able to open. However, when I try to access its datasets, it says there is an error. Is there a reason why?
The code below is used to import the folder:
hf = h5py.File('filename', 'r')
However, when I use the code below, there is an error:
x = np.array(hf["dataset"])
h5py hdf
h5py hdf
asked Nov 24 '18 at 4:21
kdfkdf
61
asked Nov 24 '18 at 4:21
kdfkdf
61
asked Nov 24 '18 at 4:21
kdfkdf
61
asked Nov 24 '18 at 4:21
kdfkdf
61
asked Nov 24 '18 at 4:21
kdfkdf
61
61
You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's adatasetcalleddataset? Or is that just a guess or random choice? How much of theh5py"getting started" documentation have you read (and understood)?
– hpaulj
Nov 24 '18 at 4:34
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest firstds = hf["dataset"]to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation,x = ds[:]is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use adumpscript to learn more.
– hpaulj
Nov 24 '18 at 5:25
add a comment |
You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's adatasetcalleddataset? Or is that just a guess or random choice? How much of theh5py"getting started" documentation have you read (and understood)?
– hpaulj
Nov 24 '18 at 4:34
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest firstds = hf["dataset"]to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation,x = ds[:]is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use adumpscript to learn more.
– hpaulj
Nov 24 '18 at 5:25
You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's a
dataset called dataset? Or is that just a guess or random choice? How much of the h5py "getting started" documentation have you read (and understood)?– hpaulj
Nov 24 '18 at 4:34
You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's a
dataset called dataset? Or is that just a guess or random choice? How much of the h5py "getting started" documentation have you read (and understood)?– hpaulj
Nov 24 '18 at 4:34
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest first
ds = hf["dataset"] to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation, x = ds[:] is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use a dump script to learn more.– hpaulj
Nov 24 '18 at 5:25
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest first
ds = hf["dataset"] to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation, x = ds[:] is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use a dump script to learn more.– hpaulj
Nov 24 '18 at 5:25
add a comment |
1 Answer
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I think you have a small syntax error. Try this (w/out np.array):
x = hf['/dataset']
I don't think you need the leading '/' to define root level, but it's good practice to include (IMHO).
If that doesn't work, it's time to double check your HDF5 contents. As hpaulj asked, are you sure dataset is at the root level? Maybe there's an intermediate group? If so, you need to define the full path to the object:
dset_table = hf['/topgroup/dataset']
I suggest you use HDFView to examine your file, or run the h5dump utility. Both are available at the HDF Group Download site. That eliminates coding questions. You can also check group names with the following:
list(hf.keys())
You should get something like this (if dataset really is at the root level):
['dataset']
Finally, you can use.get() to get the class of the object.
get(name, default=None, getclass=False, getlink=False)
Set getclass=True to get the Object class: Group or Dataset.
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
add a comment |
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1 Answer
1
active
oldest
votes
1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
I think you have a small syntax error. Try this (w/out np.array):
x = hf['/dataset']
I don't think you need the leading '/' to define root level, but it's good practice to include (IMHO).
If that doesn't work, it's time to double check your HDF5 contents. As hpaulj asked, are you sure dataset is at the root level? Maybe there's an intermediate group? If so, you need to define the full path to the object:
dset_table = hf['/topgroup/dataset']
I suggest you use HDFView to examine your file, or run the h5dump utility. Both are available at the HDF Group Download site. That eliminates coding questions. You can also check group names with the following:
list(hf.keys())
You should get something like this (if dataset really is at the root level):
['dataset']
Finally, you can use.get() to get the class of the object.
get(name, default=None, getclass=False, getlink=False)
Set getclass=True to get the Object class: Group or Dataset.
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
add a comment |
I think you have a small syntax error. Try this (w/out np.array):
x = hf['/dataset']
I don't think you need the leading '/' to define root level, but it's good practice to include (IMHO).
If that doesn't work, it's time to double check your HDF5 contents. As hpaulj asked, are you sure dataset is at the root level? Maybe there's an intermediate group? If so, you need to define the full path to the object:
dset_table = hf['/topgroup/dataset']
I suggest you use HDFView to examine your file, or run the h5dump utility. Both are available at the HDF Group Download site. That eliminates coding questions. You can also check group names with the following:
list(hf.keys())
You should get something like this (if dataset really is at the root level):
['dataset']
Finally, you can use.get() to get the class of the object.
get(name, default=None, getclass=False, getlink=False)
Set getclass=True to get the Object class: Group or Dataset.
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
add a comment |
I think you have a small syntax error. Try this (w/out np.array):
x = hf['/dataset']
I don't think you need the leading '/' to define root level, but it's good practice to include (IMHO).
If that doesn't work, it's time to double check your HDF5 contents. As hpaulj asked, are you sure dataset is at the root level? Maybe there's an intermediate group? If so, you need to define the full path to the object:
dset_table = hf['/topgroup/dataset']
I suggest you use HDFView to examine your file, or run the h5dump utility. Both are available at the HDF Group Download site. That eliminates coding questions. You can also check group names with the following:
list(hf.keys())
You should get something like this (if dataset really is at the root level):
['dataset']
Finally, you can use.get() to get the class of the object.
get(name, default=None, getclass=False, getlink=False)
Set getclass=True to get the Object class: Group or Dataset.
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
I think you have a small syntax error. Try this (w/out np.array):
x = hf['/dataset']
I don't think you need the leading '/' to define root level, but it's good practice to include (IMHO).
If that doesn't work, it's time to double check your HDF5 contents. As hpaulj asked, are you sure dataset is at the root level? Maybe there's an intermediate group? If so, you need to define the full path to the object:
dset_table = hf['/topgroup/dataset']
I suggest you use HDFView to examine your file, or run the h5dump utility. Both are available at the HDF Group Download site. That eliminates coding questions. You can also check group names with the following:
list(hf.keys())
You should get something like this (if dataset really is at the root level):
['dataset']
Finally, you can use.get() to get the class of the object.
get(name, default=None, getclass=False, getlink=False)
Set getclass=True to get the Object class: Group or Dataset.
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
answered Nov 24 '18 at 15:54
kcw78kcw78
345210
345210
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You must be doing something wrong! (if you want more help you need to give more information, like the text of the error). Do you know, for sure, that there's a
datasetcalleddataset? Or is that just a guess or random choice? How much of theh5py"getting started" documentation have you read (and understood)?– hpaulj
Nov 24 '18 at 4:34
The error says "Unable to open object (object 'signal' doesn't exist)". I am sure that the dataset is there. I read most of the h5py doucmentation, and the code above works for other data.
– kdf
Nov 24 '18 at 5:08
Why didn't you include that information initially, rather than leaving me guessing as to how much you knew or had already done! With the little you added I'd suggest first
ds = hf["dataset"]to verify that you can access the dataset. Then start displaying some properties - shape, dtype, etc.. And as per the documentation,x = ds[:]is the preferred syntax for loading. But I suspect there's something unusual about this dataset that prevents loading. If you don't know anything about it, you may have to use adumpscript to learn more.– hpaulj
Nov 24 '18 at 5:25