Merge pull request #288 from tzukpolinsky/master

changes for python 3.9 and python 3.10

requirements.txt

@@ -1,38 +1,39 @@
-Pillow == 5.4.1
+Pillow
 pyyaml == 5.3.1
-shapely == 1.7
+shapely == 1.8
 dtreeviz == 0.8.1
 eli5 == 0.10.1
 graphviz == 0.11
 imblearn == 0.0
 imgaug == 0.4.0
 imutils == 0.5.2
-matplotlib == 3.0.3
-numpy == 1.18.1
-opencv-python == 3.4.5.20
-pandas == 0.25.3
-scikit-image == 0.14.2
-scipy == 1.5.4
+matplotlib >= 3.0.3
+numpy
+opencv-python == 3.4.16.59
+pandas
+scikit-image
+scipy
 seaborn == 0.9.0
-scikit-learn == 0.22.2
+scikit-learn
 tabulate == 0.8.3
 tqdm == 4.30.0
 xgboost == 0.90
-yellowbrick == 0.9.1
+yellowbrick
 dash == 1.14.0
 dash_color_picker == 0.0.1
 dash_core_components == 1.10.2
 dash_colorscales == 0.0.4
 dash_html_components == 1.0.3
-h5py == 2.9.0
-numba == 0.52.0
-numexpr == 2.6.9
+h5py
+numba
+numexpr
 plotly == 4.9.0
-statsmodels == 0.9.0
+statsmodels
 cefpython3 == 66.0
 pyarrow == 6.0.1
 shap == 0.35.0
-h5py==2.9.0
-tables==3.6.1
+tables>=3.6.1
 xlrd==1.2.0
 trafaret==2.1.1
+geos
+ffmpeg-python

simba/SimBA.py

@@ -85,14 +85,14 @@
 from simba.ui.pop_ups.movement_analysis_pop_up import MovementAnalysisPopUp
 from simba.ui.pop_ups.movement_analysis_time_bins_pop_up import \
     MovementAnalysisTimeBinsPopUp
-from simba.ui.pop_ups.mutual_exclusivity_pop_up import MutualExclusivityPupUp
+#from simba.ui.pop_ups.mutual_exclusivity_pop_up import MutualExclusivityPupUp
 from simba.ui.pop_ups.outlier_settings_pop_up import OutlierSettingsPopUp
 from simba.ui.pop_ups.path_plot_pop_up import PathPlotPopUp
 from simba.ui.pop_ups.pose_bp_drop_pop_up import DropTrackingDataPopUp
 from simba.ui.pop_ups.pose_reorganizer_pop_up import PoseReorganizerPopUp
 from simba.ui.pop_ups.pup_retrieval_pop_up import PupRetrievalPopUp
 from simba.ui.pop_ups.quick_path_plot_pop_up import QuickLineplotPopup
-from simba.ui.pop_ups.remove_roi_features_pop_up import RemoveROIFeaturesPopUp
+#from simba.ui.pop_ups.remove_roi_features_pop_up import RemoveROIFeaturesPopUp
 from simba.ui.pop_ups.roi_analysis_pop_up import ROIAnalysisPopUp
 from simba.ui.pop_ups.roi_analysis_time_bins_pop_up import \
     ROIAnalysisTimeBinsPopUp
@@ -114,9 +114,9 @@
     ClipVideoPopUp, ConcatenatingVideosPopUp, ConcatenatorPopUp,
     ConvertVideoPopUp, CreateGIFPopUP, CropVideoPopUp, DownsampleVideoPopUp,
     ExtractAllFramesPopUp, ExtractAnnotationFramesPopUp, ExtractSEQFramesPopUp,
-    ExtractSpecificFramesPopUp, GreyscaleSingleVideoPopUp,
+    ExtractSpecificFramesPopUp,
     ImportFrameDirectoryPopUp, MergeFrames2VideoPopUp, MultiCropPopUp,
-    MultiShortenPopUp, SuperImposeFrameCountPopUp, VideoRotatorPopUp,
+    MultiShortenPopUp, VideoRotatorPopUp,
     VideoTemporalJoinPopUp)
 from simba.ui.pop_ups.visualize_pose_in_dir_pop_up import \
     VisualizePoseInFolderPopUp
@@ -138,39 +138,41 @@
 
 # from simba.unsupervised.unsupervised_ui import UnsupervisedGUI
 
-sys.setrecursionlimit(10**6)
+sys.setrecursionlimit(10 ** 6)
 currentPlatform = platform.system()
 
 
 class LoadProjectPopUp(object):
     def __init__(self):
-        main_frm = Toplevel()
-        main_frm.minsize(300, 200)
-        main_frm.wm_title("Load SimBA project (project_config.ini file)")
+        self.main_frm = Toplevel()
+        self.main_frm.minsize(300, 200)
+        self.main_frm.wm_title("Load SimBA project (project_config.ini file)")
 
-        load_project_frm = CreateLabelFrameWithIcon(
-            parent=main_frm,
+        self.load_project_frm = CreateLabelFrameWithIcon(
+            parent=self.main_frm,
             header="LOAD SIMBA PROJECT_CONFIG.INI",
             icon_name=Keys.DOCUMENTATION.value,
             icon_link=Links.LOAD_PROJECT.value,
         )
         self.selected_file = FileSelect(
-            load_project_frm, "Select file: ", title="Select project_config.ini file"
+            self.load_project_frm, "Select file: ", title="Select project_config.ini file"
         )
-        load_project_btn = Button(
-            load_project_frm,
+        self.load_project_btn = Button(
+            self.load_project_frm,
             text="LOAD PROJECT",
             fg="blue",
             command=lambda: self.launch_project(),
         )
 
-        load_project_frm.grid(row=0, sticky=NW)
+        self.load_project_frm.grid(row=0, sticky=NW)
         self.selected_file.grid(row=0, sticky=NW)
-        load_project_btn.grid(row=1, pady=10, sticky=NW)
+        self.load_project_btn.grid(row=1, pady=10, sticky=NW)
 
     def launch_project(self):
         check_file_exist_and_readable(file_path=self.selected_file.file_path)
         _ = SimbaProjectPopUp(config_path=self.selected_file.file_path)
+        self.load_project_frm.destroy()
+        self.main_frm.destroy()
 
 
 def wait_for_internet_connection(url):
@@ -578,14 +580,14 @@ def activate(box, *args):
                 config_path=self.config_path
             ),
         )
-        remove_roi_features_from_feature_set = Button(
-            roi_feature_frm,
-            text="REMOVE ROI FEATURES FROM FEATURE SET",
-            fg="darkred",
-            command=lambda: RemoveROIFeaturesPopUp(
-                config_path=self.config_path, dataset="features_extracted"
-            ),
-        )
+        # remove_roi_features_from_feature_set = Button(
+        #     roi_feature_frm,
+        #     text="REMOVE ROI FEATURES FROM FEATURE SET",
+        #     fg="darkred",
+        #     command=lambda: RemoveROIFeaturesPopUp(
+        #         config_path=self.config_path, dataset="features_extracted"
+        #     ),
+        # )
 
         feature_tools_frm = LabelFrame(
             tab5,
@@ -773,14 +775,14 @@ def activate(box, *args):
                 config_path=self.config_path
             ),
         )
-        remove_roi_features_from_annotation_set = Button(
-            lbl_tools_frm,
-            text="Remove ROI features from label set",
-            fg="darkred",
-            command=lambda: RemoveROIFeaturesPopUp(
-                config_path=self.config_path, dataset="targets_inserted"
-            ),
-        )
+        # remove_roi_features_from_annotation_set = Button(
+        #     lbl_tools_frm,
+        #     text="Remove ROI features from label set",
+        #     fg="darkred",
+        #     command=lambda: RemoveROIFeaturesPopUp(
+        #         config_path=self.config_path, dataset="targets_inserted"
+        #     ),
+        # )
 
         label_trainmachinemodel = CreateLabelFrameWithIcon(
             parent=tab8,
@@ -898,12 +900,12 @@ def activate(box, *args):
             fg="green",
             command=lambda: FSTTCPopUp(config_path=self.config_path),
         )
-        mutual_exclusivity = Button(
-            label_runmachinemodel,
-            text="MUTUAL EXCLUSIVITY CORRECTION",
-            fg="green",
-            command=lambda: MutualExclusivityPupUp(config_path=self.config_path),
-        )
+        # mutual_exclusivity = Button(
+        #     label_runmachinemodel,
+        #     text="MUTUAL EXCLUSIVITY CORRECTION",
+        #     fg="green",
+        #     command=lambda: MutualExclusivityPupUp(config_path=self.config_path),
+        # )
 
         label_machineresults = CreateLabelFrameWithIcon(
             parent=tab9,
@@ -1126,7 +1128,7 @@ def activate(box, *args):
         roi_feature_frm.grid(row=1, column=0, sticky=NW)
         append_roi_features_by_animal.grid(row=0, column=0, sticky=NW)
         append_roi_features_by_body_part.grid(row=1, column=0, sticky=NW)
-        remove_roi_features_from_feature_set.grid(row=2, column=0, sticky=NW)
+        #remove_roi_features_from_feature_set.grid(row=2, column=0, sticky=NW)
 
         feature_tools_frm.grid(row=2, column=0, sticky=NW)
         compute_feature_subset_btn.grid(row=0, column=0, sticky=NW)
@@ -1160,7 +1162,7 @@ def activate(box, *args):
         lbl_tools_frm.grid(row=9, column=0, sticky=NW)
         visualize_annotation_img_btn.grid(row=0, column=0, sticky=NW)
         third_party_annotations_btn.grid(row=1, column=0, sticky=NW)
-        remove_roi_features_from_annotation_set.grid(row=2, column=0, sticky=NW)
+        #remove_roi_features_from_annotation_set.grid(row=2, column=0, sticky=NW)
 
         label_trainmachinemodel.grid(row=6, sticky=W)
         button_trainmachinesettings.grid(row=0, column=0, sticky=NW, padx=5)
@@ -1181,7 +1183,7 @@ def activate(box, *args):
         button_runmachinemodel.grid(row=1, sticky=NW)
         kleinberg_button.grid(row=2, sticky=NW)
         fsttc_button.grid(row=3, sticky=NW)
-        mutual_exclusivity.grid(row=4, sticky=NW)
+        #mutual_exclusivity.grid(row=4, sticky=NW)
 
         label_machineresults.grid(row=9, sticky=W, pady=5)
         button_process_datalog.grid(row=2, column=0, sticky=W, padx=3)
@@ -1609,18 +1611,18 @@ def __init__(self):
             image=self.menu_icons["clahe"]["img"],
             command=CLAHEPopUp,
         )
-        video_process_menu.add_command(
-            label="Superimpose frame numbers on video",
-            compound="left",
-            image=self.menu_icons["trash"]["img"],
-            command=lambda: SuperImposeFrameCountPopUp(),
-        )
-        video_process_menu.add_command(
-            label="Convert to grayscale",
-            compound="left",
-            image=self.menu_icons["grey"]["img"],
-            command=lambda: GreyscaleSingleVideoPopUp(),
-        )
+        # video_process_menu.add_command(
+        #     label="Superimpose frame numbers on video",
+        #     compound="left",
+        #     image=self.menu_icons["trash"]["img"],
+        #     command=lambda: SuperImposeFrameCountPopUp(),
+        # )
+        # video_process_menu.add_command(
+        #     label="Convert to grayscale",
+        #     compound="left",
+        #     image=self.menu_icons["grey"]["img"],
+        #     command=lambda: GreyscaleSingleVideoPopUp(),
+        # )
         video_process_menu.add_command(
             label="Merge frames to video",
             compound="left",
@@ -1828,12 +1830,14 @@ def __init__(self):
 
         if OS.PYTHON_VER.value != "3.6":
             PythonVersionWarning(
-                msg=f"SimBA is not extensively tested beyond python 3.6. You are using python {OS.PYTHON_VER.value}. If you encounter errors in python>3.6, please report them on GitHub or Gitter and we will fix! (links in the help toolbar)"
+                msg=f"SimBA is not extensively tested beyond python 3.6. You are using python {OS.PYTHON_VER.value}. If you encounter errors in python>3.6, please report them on GitHub or Gitter and we will fix! (links in the help toolbar)",
+                source="python different than 3.6"
             )
 
         if not check_ffmpeg_available():
             FFMpegNotFoundWarning(
-                msg='SimBA could not find a FFMPEG installation on computer (as evaluated by "ffmpeg" returning None). SimBA works best with FFMPEG and it is recommended to install it on your computer'
+                msg='SimBA could not find a FFMPEG installation on computer (as evaluated by "ffmpeg" returning None). SimBA works best with FFMPEG and it is recommended to install it on your computer',
+                source="ffmpeg checker"
             )
 
     def restart(self):

simba/data_processors/agg_clf_calculator.py

@@ -157,7 +157,7 @@ def save(self) -> None:
         self.results_df = (
             self.results_df[
                 self.results_df["Measure"].isin(
-                    self.chosen_measures + self.video_meta_data
+                    self.chosen_measures# + self.video_meta_data
                 )
             ]
             .sort_values(by=["Video", "Classifier", "Measure"])

simba/labelling/labelling_interface.py

@@ -64,7 +64,7 @@ def __init__(
         self.frm_no, self.threshold_dict = 0, threshold_dict
         self.setting = setting
         self.play_video_script_path = os.path.join(
-            os.path.dirname(simba.__file__), "play_annotation_video.py"
+            os.path.dirname(simba.__file__), "labelling/play_annotation_video.py"
         )
         _, self.video_name, _ = get_fn_ext(filepath=file_path)
         self.features_extracted_file_path = os.path.join(
@@ -394,7 +394,7 @@ def __read_frm(self, frm_number=None):
         _, self.current_frm_npy = self.cap.read()
         self.current_frm_npy = cv2.cvtColor(self.current_frm_npy, cv2.COLOR_RGB2BGR)
         self.current_frm_pil = Image.fromarray(self.current_frm_npy)
-        self.current_frm_pil.thumbnail(self.max_frm_size, Image.ANTIALIAS)
+        self.current_frm_pil.thumbnail(self.max_frm_size, Image.LANCZOS)
         self.current_frm_pil = ImageTk.PhotoImage(
             master=self.main_window, image=self.current_frm_pil
         )

simba/mixins/pop_up_mixin.py

@@ -48,11 +48,11 @@ def __init__(
         config_path: Optional[str] = None,
         size: Tuple[int, int] = (400, 400),
     ):
-        self.main_frm = Toplevel()
-        self.main_frm.minsize(size[0], size[1])
-        self.main_frm.wm_title(title)
-        self.main_frm.lift()
-        self.main_frm = Canvas(hxtScrollbar(self.main_frm))
+        self.root = Toplevel()
+        self.root.minsize(size[0], size[1])
+        self.root.wm_title(title)
+        self.root.lift()
+        self.main_frm = Canvas(hxtScrollbar(self.root))
         self.main_frm.pack(fill="both", expand=True)
 
         self.palette_options = Options.PALETTE_OPTIONS.value

simba/mixins/train_model_mixin.py

@@ -705,7 +705,6 @@ def dviz_classification_visualization(
         :parameter List[str] class_names: List of class names. E.g., ['Attack absent', 'Attack present']
         :parameter str save_dir: Directory where to save output in csv file format.
         """
-
         clf = tree.DecisionTreeClassifier(max_depth=5, random_state=666)
         clf.fit(x_train, y_train)
         try:
@@ -1291,8 +1290,7 @@ def clf_predict_proba(
             else:
                 raise FeatureNumberMismatchError(
                     f"The model expects {clf_n_features} features. The data contains {len(x_df.columns)} features.",
-                    source=self.__class__.__name__,
-                )
+                    source=self.__class__.__name__)
         p_vals = clf.predict_proba(x_df)
         if p_vals.shape[1] != 2:
             raise ClassifierInferenceError(