Hello developers of CarDEC
Thank you for your product. Can you please help me to figure out, why the function CarDEC.model_counts() does not work in my hands? I downloaded your macaque retina data set and am trying to repeat all steps of your tutorial.
First I imported the packages. The computer returned:
2022-02-28 14:19:22.147693: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA
To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Next I defined the functions read_macaque , purity_score and find_resolution and read the data set. Then I ran CarDEC_API, and the computer returned:
Trying to set attribute .var of view, copying.
/Users/alex/opt/anaconda3/lib/python3.9/site-packages/pandas/core/indexing.py:1732: SettingWithCopyWarning:
A value is trying to be set on a copy of a slice from a DataFrame
See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy
self._setitem_single_block(indexer, value, name)
/Users/alex/opt/anaconda3/lib/python3.9/site-packages/scanpy/preprocessing/_simple.py:843: UserWarning: Revieved a view of an AnnData. Making a copy.
view_to_actual(adata)
Next CarDEC.build_model(n_clusters = 11). Returned `OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.
Next CarDEC.make_inference(). Works with no warnings.
Next CarDEC.model_counts(). An error was returned:
I'm doing this all in macOS Monterey
Python 3.9.7
pandas 1.3.4
numpy 1.20.3
scikit-learn 0.24.2 (as I understand, this is the same as sklearn, right?)
pickle-mixin 1.0.2
pytest 6.2.4 (as I understand, this is the same as shutil, right?)
scanpy 1.8.2
anndata 0.7.8
CarDEC 1.0.0
Hello developers of CarDEC Thank you for your product. Can you please help me to figure out, why the function
CarDEC.model_counts()does not work in my hands? I downloaded your macaque retina data set and am trying to repeat all steps of your tutorial. First I imported the packages. The computer returned:2022-02-28 14:19:22.147693: I tensorflow/core/platform/cpu_feature_guard.cc:151] This TensorFlow binary is optimized with oneAPI Deep Neural Network Library (oneDNN) to use the following CPU instructions in performance-critical operations: AVX2 FMA To enable them in other operations, rebuild TensorFlow with the appropriate compiler flags.
Next I defined the functions
read_macaque,purity_scoreandfind_resolutionand read the data set. Then I ranCarDEC_API, and the computer returned:Trying to set attribute .var of view, copying. /Users/alex/opt/anaconda3/lib/python3.9/site-packages/pandas/core/indexing.py:1732: SettingWithCopyWarning: A value is trying to be set on a copy of a slice from a DataFrame See the caveats in the documentation: https://pandas.pydata.org/pandas-docs/stable/user_guide/indexing.html#returning-a-view-versus-a-copy self._setitem_single_block(indexer, value, name) /Users/alex/opt/anaconda3/lib/python3.9/site-packages/scanpy/preprocessing/_simple.py:843: UserWarning: Revieved a view of an AnnData. Making a copy. view_to_actual(adata) Next
CarDEC.build_model(n_clusters = 11). Returned `OMP: Info #271: omp_set_nested routine deprecated, please use omp_set_max_active_levels instead.Next
CarDEC.make_inference(). Works with no warnings. NextCarDEC.model_counts(). An error was returned:NameError Traceback (most recent call last) /var/folders/jd/2jb1tdwj6_n78vpq2x3m686h0000gq/T/ipykernel_5205/1576722029.py in
----> 1 CarDEC.model_counts()
~/opt/anaconda3/lib/python3.9/site-packages/CarDEC/CarDEC_API.py in model_counts(self, load_weights, act, random_seed, splitseed, optimizer, keep_dispersion, num_epochs, batch_size_count, val_split, lr, decay_factor, patience_LR, patience_ES, denoise_all, denoise_list) 198 199 if denoise_all: --> 200 self.nbmodel.denoise(self.dataset, keep_dispersion, batch_size) 201 if self.LVG: 202 self.nbmodel_lvg.denoise(self.dataset, keep_dispersion, batch_size)
NameError: name 'batch_size' is not defined
I'm doing this all in macOS Monterey Python 3.9.7 pandas 1.3.4 numpy 1.20.3 scikit-learn 0.24.2 (as I understand, this is the same as sklearn, right?) pickle-mixin 1.0.2 pytest 6.2.4 (as I understand, this is the same as shutil, right?) scanpy 1.8.2 anndata 0.7.8 CarDEC 1.0.0
Do you have any idea of what is going on?
Sincerely Alex