change some formatted strings.

STOmics · Dec 4, 2024 · b33a003 · b33a003
1 parent 9a7806a
commit b33a003
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Showing 4 changed files with 60 additions and 18 deletions.
diff --git a/stereo/core/cell.py b/stereo/core/cell.py
@@ -43,6 +43,9 @@ def __init__(
             self.batch = self._set_batch(batch)
         self.cell_border = cell_border
         self.cell_point = None
+
+    def __getattr__(self, key):
+        return getattr(self._obs, key)
 
     def __contains__(self, item):
         return item in self._obs.columns
@@ -91,17 +94,17 @@ def size(self):
     def shape(self):
         return self._obs.shape
 
-    @property
-    def loc(self):
-        return self._obs.loc
+    # @property
+    # def loc(self):
+    #     return self._obs.loc
 
-    @property
-    def iloc(self):
-        return self._obs.iloc
+    # @property
+    # def iloc(self):
+    #     return self._obs.iloc
 
-    @property
-    def to_csv(self):
-        return self._obs.to_csv
+    # @property
+    # def to_csv(self):
+    #     return self._obs.to_csv
 
     @property
     def obs(self):
@@ -314,11 +317,11 @@ def __init__(
     #     else:
     #         object.__setattr__(self, key, value)
 
-    def __str__(self):
-        return str(self.__based_ann_data.obs)
+    # def __str__(self):
+    #     return str(self.__based_ann_data.obs)
 
-    def __repr__(self):
-        return self.__str__()
+    # def __repr__(self):
+    #     return self.__str__()
 
     def __getitem__(self, item):
         return self.__based_ann_data.obs[item]

diff --git a/stereo/core/gene.py b/stereo/core/gene.py
@@ -256,11 +256,11 @@ def __init__(self, based_ann_data: AnnData, gene_name: Optional[np.ndarray] = No
     #         return
     #     object.__setattr__(self, key, value)
 
-    def __str__(self):
-        return str(self.__based_ann_data.var)
+    # def __str__(self):
+    #     return str(self.__based_ann_data.var)
 
-    def __repr__(self):
-        return self.__str__()
+    # def __repr__(self):
+    #     return self.__str__()
 
     def __getitem__(self, item):
         return self.__based_ann_data.var[item]

diff --git a/stereo/core/result.py b/stereo/core/result.py
@@ -387,6 +387,7 @@ def __init__(self, data: AnnBasedStereoExpData):
         super().__init__()
         # self.__stereo_exp_data = data
         self.__based_ann_data = data.adata
+        self.__result_keys = []
 
     # @property
     # def adata(self):
@@ -557,6 +558,8 @@ def _real_set_item(self, type, key, value):
     def __setitem__(self, key, value):
         super().__setitem__(key, value)
 
+        self.__result_keys.append(key)
+
         for name_type, name_dict in AnnBasedResult.TYPE_NAMES_DICT.items():
             if key in name_dict and self._real_set_item(name_type, key, value):
                 return
@@ -757,6 +760,9 @@ def set_value(self, key, value):
                 self.__based_ann_data.uns[key] = value
         else:
             self.__based_ann_data.uns[key] = value
+
+    def keys(self):
+        return self.__result_keys
 
 
 class MSDataPipeLineResult(dict):

diff --git a/stereo/core/stereo_exp_data.py b/stereo/core/stereo_exp_data.py
@@ -856,7 +856,40 @@ def __init__(
         self.file_format = 'h5ad'
 
     def __str__(self):
-        return str(self._ann_data)
+        # return str(self._ann_data)
+        format_str = f"AnnBasedStereoExpData object with n_cells X n_genes = {self.shape[0]} X {self.shape[1]}"
+        format_str += f"\nadata: {id(self._ann_data)}"
+        format_str += f"\nbin_type: {self.bin_type}"
+        if self.bin_type == 'bins':
+            format_str += f"\n{'bin_size: %d' % self.bin_size}"
+        format_str += f"\noffset_x = {self.offset_x}"
+        format_str += f"\noffset_y = {self.offset_y}"
+        format_str += str(self.cells)
+        format_str += str(self.genes)
+        if self.cells_matrix:
+            format_str += f"\ncells_matrix = {list(self.cells_matrix.keys())}"
+        if self.genes_matrix:
+            format_str += f"\ngenes_matrix = {list(self.genes_matrix.keys())}"
+        if self.cells_pairwise:
+            format_str += f"\ncells_pairwise = {list(self.cells_pairwise.keys())}"
+        if self.genes_pairwise:
+            format_str += f"\ngenes_pairwise = {list(self.genes_pairwise.keys())}"
+        format_str += f"\n{str(self.layers)}"
+        format_key_record = {
+            key: value
+            for key, value in self.tl.key_record.items() if value
+        }
+        if format_key_record:
+            format_str += f"\nkey_record: {format_key_record}"
+        result_key = []
+        for rks in self.tl.key_record.values():
+            if rks is not None and len(rks) > 0:
+                result_key += rks
+        for rk in self.tl.result.keys():
+            if rk not in result_key:
+                result_key.append(rk)
+        format_str += f"\nresult: {result_key}"
+        return format_str
 
     def __repr__(self):
         return self.__str__()