{"id":15611648,"url":"https://github.com/primozgodec/fish-tracing","last_synced_at":"2025-03-29T15:11:24.509Z","repository":{"id":80114407,"uuid":"136168461","full_name":"PrimozGodec/fish-tracing","owner":"PrimozGodec","description":"Scripts fro plotting fish traces","archived":false,"fork":false,"pushed_at":"2019-11-04T20:08:23.000Z","size":27508,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-02-04T15:48:47.034Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/PrimozGodec.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2018-06-05T11:38:58.000Z","updated_at":"2019-11-04T20:08:25.000Z","dependencies_parsed_at":null,"dependency_job_id":"6b22f354-0989-483d-89cb-7cd4ebf6ee04","html_url":"https://github.com/PrimozGodec/fish-tracing","commit_stats":{"total_commits":16,"total_committers":1,"mean_commits":16.0,"dds":0.0,"last_synced_commit":"078bcb78f62b805aaa01c54017d2ab60fd8ed096"},"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PrimozGodec%2Ffish-tracing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PrimozGodec%2Ffish-tracing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PrimozGodec%2Ffish-tracing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/PrimozGodec%2Ffish-tracing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/PrimozGodec","download_url":"https://codeload.github.com/PrimozGodec/fish-tracing/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246200319,"owners_count":20739566,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-03T06:06:13.653Z","updated_at":"2025-03-29T15:11:24.476Z","avatar_url":"https://github.com/PrimozGodec.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Fish tracing\n\nScripts fro plotting fish traces\n\n## Instalation\n\nThis step need to be done only first time using this script on the machine.\n\n1. Open the `Terminal` app\n\n2. Install Python\n\n   #### MacOS\n   \n   Check if `Homebrew` is installed with typing in the Terminal:\n   \n       brew help\n\n   If you get `command not found` output then install brew:\n   \n       /usr/bin/ruby -e \"$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)\"\n       \n   If not then install `Python`:\n   \n       brew install python3\n       \n   ### Windows\n   \n   Go to https://www.python.org/downloads/ and download and install the latest \n   version of `Python`.\n   \n3. If Terminal (MacOS or Linux) or Command prompt (Windows) is not open yet\n   open it:\u003cbr\u003e\n   \n4. Install `virtualenv`:\n\n       sudo pip install virtualenv\n       \n   While installing you will be asked for a password. Type your user account \n   password. \n   \n   Create the virtual environment:\n   \n       virtualenv -p python3 ~/venv/fish_tracing\n   \n   `~/venv/fish_tracing` can be replaced with a custom path.\n   \n5. Activate the virtual environment:\n\n       source ~/venv/fish_tracing/bin/activate\n       \n6. Move to the package directory:\n\n       cd \u003cpath\u003e\n       \n7. Install requirements\n\n       pip install -r requirements.txt\n       \n## Usage\n\n1. Mac or Linux: open the Terminal app. At MacOS: cmd+space, then type Terminal\u003cbr\u003e\n   Windows: open the command prompt.\n\n2. Activate the virtual environment:\n\n       source ~/venv/fish_tracking/bin/activate\n\n3. Move to the package directory:\n\n       cd \u003cpath\u003e\n\n   e.g.\n\n       cd fish-tracking\n\n5. Run the tracing script:\n\n       python trace_fish_new.py --source \u003csource dir\u003e\n\n   e.g.\n\n       python trace_fish_new.py --source \"data/input/12 Areana Trial 1.xlsx\"\n\n   `\u003csource dir\u003e` is the path to the directory with the excel files. \u003cbr\u003e\n\n   There are two additional arguments that can be used.\n\n   `--start` defines the second when we start to plot traces (default 0).\n   E.g. value 0 means that we start to plot traces 0 seconds after the start\n   of the recording \u003cbr\u003e\n   `--end` defines the second when we end to plot traces (default 1000).\n   E.g. value 10000 means that we end to plot traces 10000 seconds\n   after the start of the recording.\n\n6. Results are now available in `data/output` directory.\n\n\n## Usage of old script `trace_fish.py`\n\n1. Mac or Linux: open the Terminal app:  cmd+space, then type Terminal\u003cbr\u003e\n   Windows: open the command prompt.\n\n2. Activate the virtual environment:\n\n       source ~/venv/fish_tracking/bin/activate\n\n3. Move to the package directory:\n\n       cd \u003cpath\u003e\n\n   e.g.\n\n       cd Downloads/Tracking\\ Instructions\\ and\\ Script/fish-tracking\n       \n4. Copy excel files with traces to the package subdirectory (`\u003csource dir\u003e`).\n\n5. Run the tracing script:\n\n       python trace_fish.py --source \u003csource dir\u003e --destination \u003cdestination dir\u003e\n\n   e.g.\n\n       python trace_fish.py --source 3-08-15\\ Nicotine\\ Experiment/Export\\ Files/ --destination 3-08-15\\ Nicotine\\ Experiment/Orange_Generated_Tracings\n       \n   `\u003csource dir\u003e` is the path to the directory with the excel files. \u003cbr\u003e\n   `\u003cdestination dir\u003e` is the path to the directory where results files will be saved\n   \n   There are two additional arguments that can be used when default settings\n   are sufficient.\n   \n   `--start` defines the second when we start to plot traces (default 10).\n   E.g. value 10 means that we start to plot traces 10 seconds after the start\n   of the recording \u003cbr\u003e\n   `--end` defines the second when we end to plot traces (default 600).\n   E.g. value 600 means that we end to plot traces 600 seconds (10 minutes) \n   after the start of the recording.\n   \n6. Results are now available at `\u003cdestination dir\u003e`.    \n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fprimozgodec%2Ffish-tracing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fprimozgodec%2Ffish-tracing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fprimozgodec%2Ffish-tracing/lists"}