Closed anemartinezlarrinaga2898 closed 1 year ago
This is the code Im using:
import os
import anndata
from scipy import io
import numpy as np
import pandas as pd
import re
import celltypist
from celltypist import models
import scanpy as sc
os.chdir("/Users/amartinezl/Library/CloudStorage/OneDrive-JosepCarrerasLeukaemiaResearchInstitute(IJC)/2_PhD/2_CELLULAR_SYSTEMS_GENOMICS/3_MEREU_PBMC_IMMUNE_ATLAS/1_ANALISIS/5_AnalisisFetal/AnotacionesCellTypist/")
os.getcwd()
def CellClasificatioin_OwnModel(data_train,data_query,model,cell_type_label):
print("Working with your own Model")
predictions = celltypist.annotate(data_query, model = new_model , majority_voting = True)
adata = predictions.to_adata()
metadata=adata.obs
return {'predictions_metadata': metadata, 'adata': adata}
path_data_query="4_PrediccionesCellTypist_Compartments/0_Data" # The fetal objects
path_data_train="5_PythonData_AdultImmune/PythonFiles" # The adult immune atlas
cell_type_label="Annot_Layer_3_Short_Name"
data_train = sc.read_h5ad(f"{path_data_train}/CellTypistFormat_AnnData_AdultImmuneAtlas.h5ad")
metadata=data_train.obs
metadata_cell_label=metadata[["barcode","Annot_Layer_3_Long_Name"]]
#anndata_path = f"{path_data_train}/CellTypistFormat_AnnData_AdultImmuneAtlas.h5ad"
metadata_cell_label=np.array(metadata_cell_label["Annot_Layer_3_Long_Name"])
new_model = celltypist.train(data_train, labels = "Annot_Layer_3_Long_Name", n_jobs = -1, feature_selection = True)
Using it in a Mac System
Hi @anemartinezlarrinaga2898 it doesn't look like a explicit CellTypist error, but more of a scikit-learn/OpenMP issue (see https://github.com/scikit-learn/scikit-learn/pull/15020 and https://github.com/ContinuumIO/anaconda-issues/issues/11294).
Are you running this on a M1/M2 Mac? May be related to the architecture. Can I ask you to show me the output of clang -v
?
Hi,
Yes I realized is not a CellTypist error because Im not able also to run the example in the tutorial.
output clang -v
-->
Apple clang version 13.0.0 (clang-1300.0.27.3)
Target: arm64-apple-darwin21.3.0
Thread model: posix
InstalledDir: /Library/Developer/CommandLineTools/usr/bin
Im running it with the new architecture
I'm not sure of a workaround for ARM architecture. There may be some useful information for you to try here: https://forum.image.sc/t/napari-tensorflow-aicsimageio-stardist-care-n2v-pyclesperanto-running-native-on-apple-silicon-m1/55051/3
Otherwise, can I suggest you try this on Google Colab?
Ok!
Will try on Google Colab! And if it does not work will try on the cluster of mi institut
Thanks!
@anemartinezlarrinaga2898, I will close this issue for now. If you still have problems, please let us know or feel free to reopen it.
Hello : )
Im trying to run cell typist with my own model and in the step "Training data using SGD logistic regression" I get the following error:
Anyone has faced this error before?
Thanks!