diff --git a/404.html b/404.html index 5cf39c13..0cde2353 100644 --- a/404.html +++ b/404.html @@ -5,7 +5,7 @@ Page Not Found | VAME - + diff --git a/assets/js/04a8f406.31392b8a.js b/assets/js/04a8f406.432dd89d.js similarity index 51% rename from assets/js/04a8f406.31392b8a.js rename to assets/js/04a8f406.432dd89d.js index 93dcc48b..9f35134b 100644 --- a/assets/js/04a8f406.31392b8a.js +++ b/assets/js/04a8f406.432dd89d.js @@ -1 +1 @@ -"use strict";(self.webpackChunkdocs=self.webpackChunkdocs||[]).push([[88],{445:(e,n,t)=>{t.r(n),t.d(n,{assets:()=>l,contentTitle:()=>o,default:()=>p,frontMatter:()=>s,metadata:()=>c,toc:()=>a});var i=t(4848),r=t(8453);const s={sidebar_label:"new",title:"vame.initialize_project.new"},o=void 0,c={id:"reference/vame/initialize_project/new",title:"vame.initialize_project.new",description:"Variational Animal Motion Embedding 1.0-alpha Toolbox",source:"@site/docs/reference/vame/initialize_project/new.md",sourceDirName:"reference/vame/initialize_project",slug:"/reference/vame/initialize_project/new",permalink:"/VAME/docs/reference/vame/initialize_project/new",draft:!1,unlisted:!1,tags:[],version:"current",frontMatter:{sidebar_label:"new",title:"vame.initialize_project.new"},sidebar:"docsSidebar",previous:{title:"videowriter",permalink:"/VAME/docs/reference/vame/analysis/videowriter"},next:{title:"logger",permalink:"/VAME/docs/reference/vame/logging/logger"}},l={},a=[{value:"init_new_project",id:"init_new_project",level:4}];function d(e){const n={a:"a",code:"code",em:"em",h4:"h4",li:"li",p:"p",pre:"pre",strong:"strong",ul:"ul",...(0,r.R)(),...e.components};return(0,i.jsxs)(i.Fragment,{children:[(0,i.jsx)(n.p,{children:"Variational Animal Motion Embedding 1.0-alpha Toolbox\n\xa9 K. 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e={5354:0,1869:0};o.f.j=(a,f)=>{var c=o.o(e,a)?e[a]:void 0;if(0!==c)if(c)f.push(c[2]);else if(/^(1869|5354)$/.test(a))e[a]=0;else{var t=new Promise(((f,t)=>c=e[a]=[f,t]));f.push(c[2]=t);var d=o.p+o.u(a),r=new Error;o.l(d,(f=>{if(o.o(e,a)&&(0!==(c=e[a])&&(e[a]=void 0),c)){var t=f&&("load"===f.type?"missing":f.type),d=f&&f.target&&f.target.src;r.message="Loading chunk "+a+" failed.\n("+t+": "+d+")",r.name="ChunkLoadError",r.type=t,r.request=d,c[1](r)}}),"chunk-"+a,a)}},o.O.j=a=>0===e[a];var a=(a,f)=>{var c,t,d=f[0],r=f[1],b=f[2],n=0;if(d.some((a=>0!==e[a]))){for(c in r)o.o(r,c)&&(o.m[c]=r[c]);if(b)var i=b(o)}for(a&&a(f);n Archive | VAME - + diff --git a/blog/index.html b/blog/index.html index 4e8299b0..a9173ce8 100644 --- a/blog/index.html +++ b/blog/index.html @@ -5,7 +5,7 @@ Blog | VAME - + diff --git a/blog/tags/blog/index.html b/blog/tags/blog/index.html index c6f77e1c..a6939e3d 100644 --- a/blog/tags/blog/index.html +++ b/blog/tags/blog/index.html @@ -5,7 +5,7 @@ One post tagged with "blog" | VAME - + diff --git a/blog/tags/index.html b/blog/tags/index.html index 76989c8a..8607d9d0 100644 --- a/blog/tags/index.html +++ b/blog/tags/index.html @@ -5,7 +5,7 @@ Tags | VAME - + diff --git a/blog/tags/vame/index.html b/blog/tags/vame/index.html index 54c33763..77077719 100644 --- a/blog/tags/vame/index.html +++ b/blog/tags/vame/index.html @@ -5,7 +5,7 @@ One post tagged with "vame" | VAME - + diff --git a/blog/welcome/index.html b/blog/welcome/index.html index e4070c92..c331bf04 100644 --- a/blog/welcome/index.html +++ b/blog/welcome/index.html @@ -5,7 +5,7 @@ Welcome | VAME - + diff --git a/docs/category/api-reference/index.html b/docs/category/api-reference/index.html index 91b5d2f2..479e3118 100644 --- a/docs/category/api-reference/index.html +++ b/docs/category/api-reference/index.html @@ -5,7 +5,7 @@ API reference | VAME - + diff --git a/docs/category/getting-started/index.html b/docs/category/getting-started/index.html index b5d44c87..4fc7c3b2 100644 --- a/docs/category/getting-started/index.html +++ b/docs/category/getting-started/index.html @@ -5,7 +5,7 @@ Getting Started | VAME - + diff --git a/docs/faq/index.html b/docs/faq/index.html index 2c83abe6..af096a2c 100644 --- a/docs/faq/index.html +++ b/docs/faq/index.html @@ -5,7 +5,7 @@ FAQ | VAME - + diff --git a/docs/getting_started/installation/index.html b/docs/getting_started/installation/index.html index 5b2534de..239f8cbc 100644 --- a/docs/getting_started/installation/index.html +++ b/docs/getting_started/installation/index.html @@ -5,7 +5,7 @@ Installation | VAME - + diff --git a/docs/getting_started/running/index.html b/docs/getting_started/running/index.html index cfc8dc73..c876e97b 100644 --- a/docs/getting_started/running/index.html +++ b/docs/getting_started/running/index.html @@ -5,7 +5,7 @@ Running VAME Workflow | VAME - + diff --git a/docs/intro/index.html b/docs/intro/index.html index dc2c14c7..12bffe4b 100644 --- a/docs/intro/index.html +++ b/docs/intro/index.html @@ -5,7 +5,7 @@ Introduction | VAME - + diff --git a/docs/reference/vame/analysis/community_analysis/index.html b/docs/reference/vame/analysis/community_analysis/index.html index 8ee42670..9843ef60 100644 --- a/docs/reference/vame/analysis/community_analysis/index.html +++ b/docs/reference/vame/analysis/community_analysis/index.html @@ -5,7 +5,7 @@ vame.analysis.community_analysis | VAME - + @@ -159,7 +159,7 @@

  • List[np.ndarray] - List of cohort community labels for each file.

    • community​

    -
    @save_state(model=CommunityFunctionSchema)
    def community(config: str,
                  cohort: bool = True,
                  cut_tree: int | None = None,
                  save_logs: bool = False) -> None
    +
    @save_state(model=CommunityFunctionSchema)
    def community(config: str,
                  parametrization: Parametrizations,
                  cohort: bool = True,
                  cut_tree: int | None = None,
                  save_logs: bool = False) -> None

    Perform community analysis.

    Arguments:

      diff --git a/docs/reference/vame/analysis/generative_functions/index.html b/docs/reference/vame/analysis/generative_functions/index.html index 94e6dfef..e77fab03 100644 --- a/docs/reference/vame/analysis/generative_functions/index.html +++ b/docs/reference/vame/analysis/generative_functions/index.html @@ -5,7 +5,7 @@ vame.analysis.generative_functions | VAME - + @@ -63,7 +63,7 @@

      vis

      Returns:

      None

      generative_model​

      -
      @save_state(model=GenerativeModelFunctionSchema)
      def generative_model(config: str,
                           mode: str = "sampling",
                           save_logs: bool = False) -> plt.Figure
      +
      @save_state(model=GenerativeModelFunctionSchema)
      def generative_model(config: str,
                           parametrization: Parametrizations,
                           mode: str = "sampling",
                           save_logs: bool = False) -> Dict[str, plt.Figure]

      Generative model.

      Arguments:

        @@ -71,8 +71,6 @@

        generative_
      • mode str, optional - Mode for generating samples. Defaults to "sampling".

      Returns:

      -
        -
      • plt.Figure - Plot of generated samples.
        • -
      +

      Dict[str, plt.Figure]: Plots of generated samples for each parametrization.

      \ No newline at end of file diff --git a/docs/reference/vame/analysis/gif_creator/index.html b/docs/reference/vame/analysis/gif_creator/index.html index e81f5d59..981f445f 100644 --- a/docs/reference/vame/analysis/gif_creator/index.html +++ b/docs/reference/vame/analysis/gif_creator/index.html @@ -5,7 +5,7 @@ vame.analysis.gif_creator | VAME - + @@ -32,7 +32,7 @@

      create_videoReturns:

      None

      gif​

      -
      def gif(
          config: str,
          pose_ref_index: int,
          subtract_background: bool = True,
          start: int | None = None,
          length: int = 500,
          max_lag: int = 30,
          label: str = 'community',
          file_format: str = '.mp4',
          crop_size: Tuple[int, int] = (300, 300)) -> None
      +
      def gif(
          config: str,
          pose_ref_index: int,
          parametrization: Parametrizations,
          subtract_background: bool = True,
          start: int | None = None,
          length: int = 500,
          max_lag: int = 30,
          label: str = 'community',
          file_format: str = '.mp4',
          crop_size: Tuple[int, int] = (300, 300)) -> None

      Create a GIF from the given configuration.

      Arguments:

        diff --git a/docs/reference/vame/analysis/pose_segmentation/index.html b/docs/reference/vame/analysis/pose_segmentation/index.html index 0af651da..3c7da52c 100644 --- a/docs/reference/vame/analysis/pose_segmentation/index.html +++ b/docs/reference/vame/analysis/pose_segmentation/index.html @@ -5,7 +5,7 @@ vame.analysis.pose_segmentation | VAME - + diff --git a/docs/reference/vame/analysis/segment_behavior/index.html b/docs/reference/vame/analysis/segment_behavior/index.html index a476df6c..c5ba2cbd 100644 --- a/docs/reference/vame/analysis/segment_behavior/index.html +++ b/docs/reference/vame/analysis/segment_behavior/index.html @@ -5,7 +5,7 @@ vame.analysis.segment_behavior | VAME - + diff --git a/docs/reference/vame/analysis/tree_hierarchy/index.html b/docs/reference/vame/analysis/tree_hierarchy/index.html index f6f01307..7c503c6b 100644 --- a/docs/reference/vame/analysis/tree_hierarchy/index.html +++ b/docs/reference/vame/analysis/tree_hierarchy/index.html @@ -5,7 +5,7 @@ vame.analysis.tree_hierarchy | VAME - + diff --git a/docs/reference/vame/analysis/umap/index.html b/docs/reference/vame/analysis/umap/index.html index 0da56ede..f1c38819 100644 --- a/docs/reference/vame/analysis/umap/index.html +++ b/docs/reference/vame/analysis/umap/index.html @@ -5,7 +5,7 @@ vame.analysis.umap | VAME - + @@ -29,18 +29,6 @@

        umap_embeddin
        • np.ndarray - UMAP embedding.
        -

        umap_vis_community_labels​

        -
        def umap_vis_community_labels(cfg: dict, embed: np.ndarray,
                                      community_labels_all: np.ndarray,
                                      save_path: str | None) -> None
        -

        Create plotly visualizaton of UMAP embedding with community labels.

        -

        Arguments:

        -
          -
        • cfg dict - Configuration parameters.
          • -
        • embed np.ndarray - UMAP embedding.
          • -
        • community_labels_all np.ndarray - Community labels.
          • -
        • save_path - Path to save the plot. If None it will not save the plot.
          • -
        -

        Returns:

        -

        None

        umap_vis​

        def umap_vis(embed: np.ndarray, num_points: int) -> None

        Visualize UMAP embedding without labels.

        @@ -75,7 +63,7 @@

        umap_vis_comm<

        Returns:

        fig - Plot figure of UMAP visualization embedding with community labels.

        visualization​

        -
        @save_state(model=VisualizationFunctionSchema)
        def visualization(config: Union[str, Path],
                          label: Optional[str] = None,
                          save_logs: bool = False) -> None
        +
        @save_state(model=VisualizationFunctionSchema)
        def visualization(config: Union[str, Path],
                          parametrization: Parametrizations,
                          label: Optional[str] = None,
                          save_logs: bool = False) -> None

        Visualize UMAP embeddings based on configuration settings.

        Arguments:

          diff --git a/docs/reference/vame/analysis/umap_visualization/index.html b/docs/reference/vame/analysis/umap_visualization/index.html index 3d9c3f06..4bd7333f 100644 --- a/docs/reference/vame/analysis/umap_visualization/index.html +++ b/docs/reference/vame/analysis/umap_visualization/index.html @@ -5,7 +5,7 @@ vame.analysis.umap_visualization | VAME - + diff --git a/docs/reference/vame/analysis/videowriter/index.html b/docs/reference/vame/analysis/videowriter/index.html index 4f29198c..779d3b92 100644 --- a/docs/reference/vame/analysis/videowriter/index.html +++ b/docs/reference/vame/analysis/videowriter/index.html @@ -5,7 +5,7 @@ vame.analysis.videowriter | VAME - + @@ -15,7 +15,7 @@

          https://github.com/LINCellularNeuroscience/VAME Licensed under GNU General Public License v3.0

          get_cluster_vid​

          -
          def get_cluster_vid(cfg: dict,
                              path_to_file: str,
                              file: str,
                              n_cluster: int,
                              videoType: str,
                              flag: str,
                              output_video_type: str = ".mp4",
                              tqdm_logger_stream: TqdmToLogger | None = None) -> None
          +
          def get_cluster_vid(cfg: dict,
                              path_to_file: str,
                              file: str,
                              n_cluster: int,
                              videoType: str,
                              flag: str,
                              param: Parametrizations,
                              output_video_type: str = ".mp4",
                              tqdm_logger_stream: TqdmToLogger | None = None) -> None

          Generate cluster videos.

          Arguments:

            @@ -29,7 +29,7 @@

            get_cluster_

            Returns:

            None - Generate cluster videos and save them to fs on project folder.

            motif_videos​

            -
            @save_state(model=MotifVideosFunctionSchema)
            def motif_videos(config: Union[str, Path],
                             videoType: str = '.mp4',
                             output_video_type: str = '.mp4',
                             save_logs: bool = False) -> None
            +
            @save_state(model=MotifVideosFunctionSchema)
            def motif_videos(config: Union[str, Path],
                             parametrization: Parametrizations,
                             videoType: str = '.mp4',
                             output_video_type: str = '.mp4',
                             save_logs: bool = False) -> None

            Generate motif videos.

            Arguments:

              @@ -40,7 +40,7 @@

              motif_videosReturns:

              None - Generate motif videos and save them to filesystem on project cluster_videos folder.

              community_videos​

              -
              @save_state(model=CommunityVideosFunctionSchema)
              def community_videos(config: Union[str, Path],
                                   videoType: str = '.mp4',
                                   save_logs: bool = False) -> None
              +
              @save_state(model=CommunityVideosFunctionSchema)
              def community_videos(config: Union[str, Path],
                                   parametrization: Parametrizations,
                                   videoType: str = '.mp4',
                                   save_logs: bool = False,
                                   output_video_type: str = '.mp4') -> None

              Generate community videos.

              Arguments:

                diff --git a/docs/reference/vame/initialize_project/new/index.html b/docs/reference/vame/initialize_project/new/index.html index 7e9d8f75..38f252d3 100644 --- a/docs/reference/vame/initialize_project/new/index.html +++ b/docs/reference/vame/initialize_project/new/index.html @@ -5,7 +5,7 @@ vame.initialize_project.new | VAME - + @@ -22,7 +22,7 @@ https://github.com/AlexEMG/DeepLabCut/blob/master/AUTHORS Licensed under GNU Lesser General Public License v3.0

                init_new_project​

                -
                def init_new_project(project: str,
                                     videos: List[str],
                                     poses_estimations: List[str],
                                     working_directory: str = None,
                                     videotype: str = '.mp4') -> str
                +
                def init_new_project(
                        project: str,
                        videos: List[str],
                        poses_estimations: List[str],
                        working_directory: str = '.',
                        videotype: str = '.mp4',
                        paths_to_pose_nwb_series_data: Optional[str] = None) -> str

                Creates a new VAME project with the given parameters.

                Arguments:

                  diff --git a/docs/reference/vame/logging/logger/index.html b/docs/reference/vame/logging/logger/index.html index 38261fc7..8d2ff7e2 100644 --- a/docs/reference/vame/logging/logger/index.html +++ b/docs/reference/vame/logging/logger/index.html @@ -5,7 +5,7 @@ vame.logging.logger | VAME - + diff --git a/docs/reference/vame/model/create_training/index.html b/docs/reference/vame/model/create_training/index.html index b9410f97..a076f45e 100644 --- a/docs/reference/vame/model/create_training/index.html +++ b/docs/reference/vame/model/create_training/index.html @@ -5,7 +5,7 @@ vame.model.create_training | VAME - + diff --git a/docs/reference/vame/model/dataloader/index.html b/docs/reference/vame/model/dataloader/index.html index 6fc42a7e..8b8e76f7 100644 --- a/docs/reference/vame/model/dataloader/index.html +++ b/docs/reference/vame/model/dataloader/index.html @@ -5,7 +5,7 @@ vame.model.dataloader | VAME - + diff --git a/docs/reference/vame/model/evaluate/index.html b/docs/reference/vame/model/evaluate/index.html index 2163769f..f781cdab 100644 --- a/docs/reference/vame/model/evaluate/index.html +++ b/docs/reference/vame/model/evaluate/index.html @@ -5,7 +5,7 @@ vame.model.evaluate | VAME - + diff --git a/docs/reference/vame/model/rnn_model/index.html b/docs/reference/vame/model/rnn_model/index.html index d3e9e3b2..f69369b3 100644 --- a/docs/reference/vame/model/rnn_model/index.html +++ b/docs/reference/vame/model/rnn_model/index.html @@ -5,7 +5,7 @@ vame.model.rnn_model | VAME - + diff --git a/docs/reference/vame/model/rnn_vae/index.html b/docs/reference/vame/model/rnn_vae/index.html index 8e5d5cb8..14be8e9a 100644 --- a/docs/reference/vame/model/rnn_vae/index.html +++ b/docs/reference/vame/model/rnn_vae/index.html @@ -5,7 +5,7 @@ vame.model.rnn_vae | VAME - + diff --git a/docs/reference/vame/schemas/states/index.html b/docs/reference/vame/schemas/states/index.html index 03c12a3b..4c73dbac 100644 --- a/docs/reference/vame/schemas/states/index.html +++ b/docs/reference/vame/schemas/states/index.html @@ -5,7 +5,7 @@ vame.schemas.states | VAME - + diff --git a/docs/reference/vame/util/align_egocentrical/index.html b/docs/reference/vame/util/align_egocentrical/index.html index 9fde80ab..b14dfc08 100644 --- a/docs/reference/vame/util/align_egocentrical/index.html +++ b/docs/reference/vame/util/align_egocentrical/index.html @@ -5,7 +5,7 @@ vame.util.align_egocentrical | VAME - + @@ -43,7 +43,7 @@

                  play_alig
                • frame_count int - Number of frames in the video.

                alignment​

                -
                def alignment(
                        path_to_file: str,
                        filename: str,
                        pose_ref_index: List[int],
                        video_format: str,
                        crop_size: Tuple[int, int],
                        confidence: float,
                        use_video: bool = False,
                        check_video: bool = False,
                        tqdm_stream: TqdmToLogger = None
                ) -> Tuple[np.ndarray, List[np.ndarray]]
                +
                def alignment(
                        path_to_file: str,
                        filename: str,
                        pose_ref_index: List[int],
                        video_format: str,
                        crop_size: Tuple[int, int],
                        confidence: float,
                        pose_estimation_filetype: PoseEstimationFiletype,
                        path_to_pose_nwb_series_data: str = None,
                        use_video: bool = False,
                        check_video: bool = False,
                        tqdm_stream: TqdmToLogger = None
                ) -> Tuple[np.ndarray, List[np.ndarray]]

                Perform alignment of egocentric data.

                Arguments:

                  diff --git a/docs/reference/vame/util/auxiliary/index.html b/docs/reference/vame/util/auxiliary/index.html index 0b0a87e0..1bb990cb 100644 --- a/docs/reference/vame/util/auxiliary/index.html +++ b/docs/reference/vame/util/auxiliary/index.html @@ -5,7 +5,7 @@ vame.util.auxiliary | VAME - + diff --git a/docs/reference/vame/util/csv_to_npy/index.html b/docs/reference/vame/util/csv_to_npy/index.html index c75c6ded..fd10e74b 100644 --- a/docs/reference/vame/util/csv_to_npy/index.html +++ b/docs/reference/vame/util/csv_to_npy/index.html @@ -5,7 +5,7 @@ vame.util.csv_to_npy | VAME - + @@ -14,8 +14,8 @@ Leibniz Institute for Neurobiology, Magdeburg, Germany

                  https://github.com/LINCellularNeuroscience/VAME Licensed under GNU General Public License v3.0

                  -

                  csv_to_numpy​

                  -
                  @save_state(model=CsvToNumpyFunctionSchema)
                  def csv_to_numpy(config: str, save_logs=False) -> None
                  +

                  pose_to_numpy​

                  +
                  @save_state(model=PoseToNumpyFunctionSchema)
                  def pose_to_numpy(config: str, save_logs=False) -> None

                  Converts a pose-estimation.csv file to a numpy array. Note that this code is only useful for data which is a priori egocentric, i.e. head-fixed or otherwise restrained animals.

                  Raises:

                  diff --git a/docs/reference/vame/util/data_manipulation/index.html b/docs/reference/vame/util/data_manipulation/index.html index 9e6ab122..4fc92571 100644 --- a/docs/reference/vame/util/data_manipulation/index.html +++ b/docs/reference/vame/util/data_manipulation/index.html @@ -3,13 +3,25 @@ -vame.util.data_manipulation | VAME +vame.util.data_manipulation | VAME - + -

                  vame.util.data_manipulation

                  consecutive​

                  +

                  vame.util.data_manipulation

                  get_pose_data_from_nwb_file​

                  +
                  def get_pose_data_from_nwb_file(
                          nwbfile: NWBFile, path_to_pose_nwb_series_data: str) -> LabelledDict
                  +

                  Get pose data from nwb file using a inside path to the nwb data.

                  +

                  Arguments:

                  +
                    +
                  • nwbfile NWBFile - NWB file object.
                    • +
                  • path_to_pose_nwb_series_data str - Path to the pose data inside the nwb file.
                    • +
                  +

                  Returns:

                  +
                    +
                  • LabelledDict - Pose data.
                    • +
                  +

                  consecutive​

                  def consecutive(data: np.ndarray, stepsize: int = 1) -> List[np.ndarray]

                  Find consecutive sequences in the data array.

                  Arguments:

                  diff --git a/docs/reference/vame/util/gif_pose_helper/index.html b/docs/reference/vame/util/gif_pose_helper/index.html index ff231932..e636cfc1 100644 --- a/docs/reference/vame/util/gif_pose_helper/index.html +++ b/docs/reference/vame/util/gif_pose_helper/index.html @@ -5,7 +5,7 @@ vame.util.gif_pose_helper | VAME - + diff --git a/docs/reference/vame/util/model_util/index.html b/docs/reference/vame/util/model_util/index.html index b9ccc873..f017d618 100644 --- a/docs/reference/vame/util/model_util/index.html +++ b/docs/reference/vame/util/model_util/index.html @@ -5,7 +5,7 @@ vame.util.model_util | VAME - + diff --git a/index.html b/index.html index 868fbc22..e3945873 100644 --- a/index.html +++ b/index.html @@ -5,7 +5,7 @@ VAME | VAME - + diff --git a/markdown-page/index.html b/markdown-page/index.html index 7087b085..3b9cf73b 100644 --- a/markdown-page/index.html +++ b/markdown-page/index.html @@ -5,7 +5,7 @@ Markdown page example | VAME - +