From cf7610cb2aa1faac62b62973f6be362fbf3f7367 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Mon, 30 Sep 2019 19:17:43 +0200 Subject: [PATCH 01/42] #98 changed the file pointing to source url --- nwb_explorer/nwb_data_manager.py | 2 +- .../nwb_model_interpreter.py | 16 +++++++++------- webapp/components/Metadata.js | 3 ++- 3 files changed, 12 insertions(+), 9 deletions(-) diff --git a/nwb_explorer/nwb_data_manager.py b/nwb_explorer/nwb_data_manager.py index 9c2e3b1..9968bca 100644 --- a/nwb_explorer/nwb_data_manager.py +++ b/nwb_explorer/nwb_data_manager.py @@ -61,7 +61,7 @@ def get_project_from_url(self, nwbfile): except Exception as e: raise Exception("Error retrieving file" + nwbfile) from e try: - model_interpreter = NWBModelInterpreter(nwbfilename) + model_interpreter = NWBModelInterpreter(nwbfilename, source_url=nwbfile) add_model_interpreter(model_interpreter.library.id, model_interpreter) geppetto_model = model_interpreter.create_model() diff --git a/nwb_explorer/nwb_model_interpreter/nwb_model_interpreter.py b/nwb_explorer/nwb_model_interpreter/nwb_model_interpreter.py index 6f6764e..c30b1ca 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_model_interpreter.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_model_interpreter.py @@ -25,11 +25,13 @@ def assign_name_to_type(pynwb_obj): class NWBModelInterpreter(ModelInterpreter): - def __init__(self, nwb_file_name): - - logging.info(f'Creating a Model Interpreter for {nwb_file_name}') - self.nwb_file_name = nwb_file_name if isinstance(nwb_file_name, str) else 'in-memory file' - self.nwb_reader = NWBReader(nwb_file_name) + def __init__(self, nwb_file_or_filename, source_url=None): + if source_url == None: + source_url = nwb_file_or_filename + logging.info(f'Creating a Model Interpreter for {nwb_file_or_filename}') + self.nwb_file_name = nwb_file_or_filename if isinstance(nwb_file_or_filename, str) else 'in-memory file' + self.source_url = source_url + self.nwb_reader = NWBReader(nwb_file_or_filename) self.library = GeppettoLibrary(name='nwbfile', id='nwbfile') @staticmethod @@ -60,11 +62,11 @@ def importType(self, url, type_name, library, geppetto_model_access: GeppettoMod # build compositeTypes for pynwb objects root_type = mapper.create_type(self.get_nwbfile(), type_name=type_name, type_id=type_name) if isinstance(self.nwb_file_name, str) and type_name == 'nwbfile': - from nwb_explorer.nwb_data_manager import CACHE_DIRNAME + root_type.variables.append( model_factory.create_url_variable( id='source file', - url=f"{settings.home_page}/{CACHE_DIRNAME}/{os.path.basename(self.nwb_file_name)}" + url=self.source_url if 'http' in self.source_url else 'file://' + self.source_url ) ) return root_type diff --git a/webapp/components/Metadata.js b/webapp/components/Metadata.js index 4306d54..f1ff984 100644 --- a/webapp/components/Metadata.js +++ b/webapp/components/Metadata.js @@ -33,12 +33,13 @@ export default class Metadata extends React.Component { [ this.formatField('Name', type.getId()), this.formatField('Type', type.getName()), + this.formatField('Path', this.props.instancePath), this.formatField('NWB Explorer support', this.getTypeSupport(type.getName())), ] ) ); - } + } type.getChildren().forEach(variable => { From 62959e4af9bc261b1bbbc7bd57df05e48cc408d5 Mon Sep 17 00:00:00 2001 From: Afonso Pinto Date: Thu, 24 Oct 2019 11:36:43 +0200 Subject: [PATCH 02/42] Update install script --- utilities/install.py | 34 ++++++++++++++++++++++++++++++---- 1 file changed, 30 insertions(+), 4 deletions(-) diff --git a/utilities/install.py b/utilities/install.py index 69963dd..9709241 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -1,6 +1,7 @@ import os import subprocess import sys +import json branch = None @@ -62,10 +63,10 @@ def execute(cmd, cwd='.'): def main(branch=branch, skipNpm=False, skipTest=False, development=False): - + print(f"{steps()}\n") sys.stdout.flush() - + # install pytest if needed @@ -123,17 +124,42 @@ def main(branch=branch, skipNpm=False, skipTest=False, development=False): os.makedirs(css_path) execute(cmd=['cp', 'custom.css', css_path], cwd=HERE) + # Enables Compression + json_config_path = "{}/jupyter_notebook_config.json".format(config_dir) + config = {} + if os.path.exists(json_config_path): + with open(json_config_path, 'r') as f: + try: + config = json.load(f) + except Exception as e: + print("Something went wrong reading the jupyter configuration file.\n{}" + "\nNew configuration will be created".format(str(e))) + f.close() + with open(json_config_path, 'w+') as f: + try: + _ = config['NotebookApp'] + except KeyError: + config['NotebookApp'] = {'tornado_settings': {}} + try: + _ = config['NotebookApp']['tornado_settings'] + except KeyError: + config['NotebookApp']['tornado_settings'] = {} + config['NotebookApp']['tornado_settings']['gzip'] = True + f.seek(0) + json.dump(config, f) + f.truncate() + # test if skipTest: cprint("Skipping tests") else: cprint("Testing NWB-Explorer") - execute(cmd=['python', '-m', 'pytest', + execute(cmd=['python', '-m', 'pytest', '--ignore=dependencies', '--ignore=test/test_reader.py', ], cwd=ROOT_DIR) - + cprint("Installing client packages") if not skipNpm: execute(cmd=['npm', 'install'], cwd=WEBAPP_DIR) From e9cae258340c0f41c7154ed1c4e072c733dee1dd Mon Sep 17 00:00:00 2001 From: Afonso Pinto Date: Thu, 24 Oct 2019 11:48:34 +0200 Subject: [PATCH 03/42] Make json prettier --- utilities/install.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/utilities/install.py b/utilities/install.py index 9709241..37cfcca 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -146,7 +146,7 @@ def main(branch=branch, skipNpm=False, skipTest=False, development=False): config['NotebookApp']['tornado_settings'] = {} config['NotebookApp']['tornado_settings']['gzip'] = True f.seek(0) - json.dump(config, f) + json.dump(config, f, indent=4, sort_keys=True) f.truncate() # test From 365f0e9a52b38ab5546d4603a3631df0cfda44ef Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Mon, 25 Nov 2019 14:00:56 +0000 Subject: [PATCH 04/42] Updates to Docker info & links in about. --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 639f855..7e599a8 100644 --- a/README.md +++ b/README.md @@ -93,14 +93,14 @@ To check if a dependency is installed in development mode, run `pip list`. ### Run via Docker -There is a dockerfile ready to build a container for NWB-Explorer: +There is a [Dockerfile](./Dockerfile) ready to build a container for NWB-Explorer: ```bash -cd nwb-explorer/k8s +cd nwb-explorer docker build -t nwb-explorer . docker run -it -p8888:8888 nwb-explorer ``` -Then, after the docker contained has started, the application is ready http://localhost:8888/geppetto +Then, after the Docker contained has started, the application is ready at http://localhost:8888 ## Built With @@ -111,11 +111,11 @@ Then, after the docker contained has started, the application is ready http://lo ## Background -The NWB Explorer was initially created by MetaCell to showcase the features of the Geppetto platform to share -neurophysiological data in Neurodata Without Borders format. It was further developed as part of a -Google Summer of Code project with the OpenWorm project. It is currently being extended as part of the Open Source Brain +The NWB Explorer was initially created by [MetaCell](http://metacell.us) to showcase the features of the [Geppetto](http://www.geppetto.org/) platform to share +neurophysiological data in [Neurodata Without Borders](https://www.nwb.org/) format. It was further developed as part of a +[Google Summer of Code](https://summerofcode.withgoogle.com/) project for the [OpenWorm project](http://openworm.org/). It is currently being extended as part of the [Open Source Brain](http://www.opensourcebrain.org/) project to provide both a standalone and online application for visualising and analysing the contents of NWB:N 2 files. -This work is currently funded by the Wellcome Trust. +This work is currently funded by the [Wellcome Trust](https://wellcome.ac.uk/). ## Authors From 1dae87acbd96d5ce6bb3f3ace35965f699030c20 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Thu, 6 Feb 2020 12:01:46 +0100 Subject: [PATCH 05/42] #133 Fix installation on docker --- Dockerfile | 3 +++ utilities/install.py | 2 +- 2 files changed, 4 insertions(+), 1 deletion(-) diff --git a/Dockerfile b/Dockerfile index 89401ee..1d3da38 100644 --- a/Dockerfile +++ b/Dockerfile @@ -5,6 +5,9 @@ ENV FOLDER=nwb-explorer USER root RUN apt-get update -qq &&\ apt-get install python3-tk vim nano unzip -qq +RUN npm i -g npm@6 + +RUN chown -R 1000:100 $HOME/.npm USER $NB_UID RUN jupyter labextension disable @jupyterlab/hub-extension diff --git a/utilities/install.py b/utilities/install.py index 37cfcca..4fb22ae 100644 --- a/utilities/install.py +++ b/utilities/install.py @@ -162,7 +162,7 @@ def main(branch=branch, skipNpm=False, skipTest=False, development=False): cprint("Installing client packages") if not skipNpm: - execute(cmd=['npm', 'install'], cwd=WEBAPP_DIR) + execute(cmd=['npm', 'install' if development else 'ci'], cwd=WEBAPP_DIR) execute(cmd=['npm', 'run', 'build-dev' if development else 'build'], cwd=WEBAPP_DIR) From 14bf85f450f98b9ed73d7976e21229719e80598b Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Thu, 6 Feb 2020 12:09:01 +0100 Subject: [PATCH 06/42] Update nodejs for travis --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index afb485a..f71bd91 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: node_js node_js: - - "9" + - "13" cache: - pip - npm From 7c36234765ba1c4d49c1acb9b76943bb082a3e2c Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Fri, 14 Feb 2020 13:43:20 +0000 Subject: [PATCH 07/42] Minor text/url changes --- webapp/components/FileUrlSelector.js | 2 +- webapp/components/pages/SplashPage.js | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/webapp/components/FileUrlSelector.js b/webapp/components/FileUrlSelector.js index 09f96be..aac40b6 100644 --- a/webapp/components/FileUrlSelector.js +++ b/webapp/components/FileUrlSelector.js @@ -35,7 +35,7 @@ export default class FileUrlSelector extends React.Component {
From 78435b539a1ba5b636068d975f4f3bd9bada51af Mon Sep 17 00:00:00 2001 From: jrmartin Date: Tue, 25 Feb 2020 10:49:39 -0600 Subject: [PATCH 08/42] Make arrows/download/play icons more visible --- webapp/components/ImageViewer.js | 10 ++++---- webapp/package-lock.json | 39 +++++++++----------------------- webapp/styles/main.less | 8 +++---- 3 files changed, 20 insertions(+), 37 deletions(-) diff --git a/webapp/components/ImageViewer.js b/webapp/components/ImageViewer.js index 63a786c..cef60f5 100644 --- a/webapp/components/ImageViewer.js +++ b/webapp/components/ImageViewer.js @@ -19,12 +19,12 @@ const styles = theme => ({ pointerEvents: "none" }, arrowRight: { - opacity: 0.5, + opacity: 1.0, marginRight: "10px", pointerEvents: "none" }, arrowLeft: { - opacity: 0.5, + opacity: 1.0, marginLeft: "10px", pointerEvents: "none" }, @@ -47,14 +47,14 @@ const styles = theme => ({ }, download: { top: "20px", - left: "48px", - opacity: 0.5, + left: "50px", + opacity: 1.0, position: "absolute" }, play: { top: "20px", left: "24px", - opacity: 0.5, + opacity: 1.0, position: "absolute" } diff --git a/webapp/package-lock.json b/webapp/package-lock.json index b7f8b44..2e77217 100644 --- a/webapp/package-lock.json +++ b/webapp/package-lock.json @@ -1,6 +1,6 @@ { "name": "nwb-explorer", - "version": "0.2.0", + "version": "0.3.0", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -892,7 +892,7 @@ "file-loader": "^2.0.0", "file-saver": "^1.3.3", "google-maps": "^3.2.1", - "griddle-0.6-fork": "git+https://github.com/rodriguez-facundo/griddle.git", + "griddle-0.6-fork": "git+https://github.com/rodriguez-facundo/griddle.git#218468b8c438295f8b3c6a8229491eb7972ed85e", "griddle-react": "^1.13.1", "handlebars": "^4.0.5", "html2canvas": "^1.0.0-alpha.12", @@ -21094,8 +21094,7 @@ }, "ansi-regex": { "version": "2.1.1", - "bundled": true, - "optional": true + "bundled": true }, "aproba": { "version": "1.2.0", @@ -21132,8 +21131,7 @@ }, "code-point-at": { "version": "1.1.0", - "bundled": true, - "optional": true + "bundled": true }, "concat-map": { "version": "0.0.1", @@ -21142,8 +21140,7 @@ }, "console-control-strings": { "version": "1.1.0", - "bundled": true, - "optional": true + "bundled": true }, "core-util-is": { "version": "1.0.2", @@ -21246,8 +21243,7 @@ }, "inherits": { "version": "2.0.3", - "bundled": true, - "optional": true + "bundled": true }, "ini": { "version": "1.3.5", @@ -21257,7 +21253,6 @@ "is-fullwidth-code-point": { "version": "1.0.0", "bundled": true, - "optional": true, "requires": { "number-is-nan": "^1.0.0" } @@ -21283,7 +21278,6 @@ "minipass": { "version": "2.3.5", "bundled": true, - "optional": true, "requires": { "safe-buffer": "^5.1.2", "yallist": "^3.0.0" @@ -21300,7 +21294,6 @@ "mkdirp": { "version": "0.5.1", "bundled": true, - "optional": true, "requires": { "minimist": "0.0.8" } @@ -21384,7 +21377,6 @@ "once": { "version": "1.4.0", "bundled": true, - "optional": true, "requires": { "wrappy": "1" } @@ -21460,8 +21452,7 @@ }, "safe-buffer": { "version": "5.1.2", - "bundled": true, - "optional": true + "bundled": true }, "safer-buffer": { "version": "2.1.2", @@ -21491,7 +21482,6 @@ "string-width": { "version": "1.0.2", "bundled": true, - "optional": true, "requires": { "code-point-at": "^1.0.0", "is-fullwidth-code-point": "^1.0.0", @@ -21509,7 +21499,6 @@ "strip-ansi": { "version": "3.0.1", "bundled": true, - "optional": true, "requires": { "ansi-regex": "^2.0.0" } @@ -21548,13 +21537,11 @@ }, "wrappy": { "version": "1.0.2", - "bundled": true, - "optional": true + "bundled": true }, "yallist": { "version": "3.0.3", - "bundled": true, - "optional": true + "bundled": true } } }, @@ -22560,7 +22547,6 @@ "version": "2.3.5", "bundled": true, "dev": true, - "optional": true, "requires": { "safe-buffer": "^5.1.2", "yallist": "^3.0.0" @@ -22579,7 +22565,6 @@ "version": "0.5.1", "bundled": true, "dev": true, - "optional": true, "requires": { "minimist": "0.0.8" } @@ -22759,8 +22744,7 @@ "safe-buffer": { "version": "5.1.2", "bundled": true, - "dev": true, - "optional": true + "dev": true }, "safer-buffer": { "version": "2.1.2", @@ -22866,8 +22850,7 @@ "yallist": { "version": "3.0.3", "bundled": true, - "dev": true, - "optional": true + "dev": true } } }, diff --git a/webapp/styles/main.less b/webapp/styles/main.less index d4348bb..df45e2e 100644 --- a/webapp/styles/main.less +++ b/webapp/styles/main.less @@ -575,12 +575,12 @@ iframe{ } .imgBtn { - font-size: medium!important; - color: grey!important; + font-size: large!important; + color: #07de07!important; } .imgBtn:hover{ - color: white!important; - opacity: 0.9 + color: #07de07!important; + opacity: 1.0 } From 550e5f63761ddc02bf1da5d78172cacaf2489d7b Mon Sep 17 00:00:00 2001 From: jrmartin Date: Tue, 25 Feb 2020 11:58:19 -0600 Subject: [PATCH 09/42] Make Docker installation be first suggestion in instructions --- README.md | 35 +++++++++++++++++++++-------------- 1 file changed, 21 insertions(+), 14 deletions(-) diff --git a/README.md b/README.md index 7e599a8..bce8406 100644 --- a/README.md +++ b/README.md @@ -39,19 +39,37 @@ conda create -n nwb-explorer python=3.7 conda activate nwb-explorer ``` -### Local installation +### Clone 'nwb-explorer' repository -Instructions to get a development environment running. +Clone repository using the development branch: ```bash git clone -b development https://github.com/MetaCell/nwb-explorer +``` + +### Run via Docker + +There is a [Dockerfile](./Dockerfile) ready to build a container for NWB-Explorer: + +```bash +cd nwb-explorer +docker build -t nwb-explorer . +docker run -it -p8888:8888 nwb-explorer +``` +Then, after the Docker contained has started, the application is ready at http://localhost:8888 + +### Local installation without Docker + +Instructions to get a development environment running. + +```bash cd nwb-explorer python utilities/install.py ``` ## How to run NWB Explorer -After the installation is complete, run the script: +After the local installation is complete, run the script: ```bash cd nwb-explorer @@ -91,17 +109,6 @@ This will spawn a process that while left running will watch for any changes on To check if a dependency is installed in development mode, run `pip list`. -### Run via Docker - -There is a [Dockerfile](./Dockerfile) ready to build a container for NWB-Explorer: - -```bash -cd nwb-explorer -docker build -t nwb-explorer . -docker run -it -p8888:8888 nwb-explorer -``` -Then, after the Docker contained has started, the application is ready at http://localhost:8888 - ## Built With * [Geppetto](http://www.geppetto.org/) - Used to build a web-based application to interpret and visualize the NWB:N 2 files. From 6dc7e28ee1ded3c311e0dbcf7a43a262093cf4f3 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Tue, 25 Feb 2020 13:06:46 -0600 Subject: [PATCH 10/42] Align play icon to left arrow, remove download link in general bar, add text to python console, some readme.md clean up --- README.md | 6 +++--- nwb_explorer/api.py | 2 ++ webapp/components/ImageViewer.js | 4 ++-- webapp/components/Metadata.js | 2 +- 4 files changed, 8 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index bce8406..5bf0f40 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ conda create -n nwb-explorer python=3.7 conda activate nwb-explorer ``` -### Clone 'nwb-explorer' repository +### Clone "nwb-explorer" Repository Clone repository using the development branch: @@ -58,7 +58,7 @@ docker run -it -p8888:8888 nwb-explorer ``` Then, after the Docker contained has started, the application is ready at http://localhost:8888 -### Local installation without Docker +### Local Installation without Docker Instructions to get a development environment running. @@ -99,7 +99,7 @@ pip install -e . ### Javascript code from sources -JS/HTML code can be found inside `static/org.geppetto.frontend/src/main/webapp/`. The code needs to be rebuilt with webpack everytime there is a change. To avoid having to do so you can use the Webpack development server running in `/static/org.geppetto.frontend/src/main/webapp/` this command: +JS/HTML code can be found inside `webapp/`. The code needs to be rebuilt with webpack everytime there is a change. To avoid having to do so you can use the Webpack development server running in `webapp/` this command: ```bash npm run build-dev-noTest:watch diff --git a/nwb_explorer/api.py b/nwb_explorer/api.py index 4495f0b..27e8832 100644 --- a/nwb_explorer/api.py +++ b/nwb_explorer/api.py @@ -29,6 +29,8 @@ def createNotebook(filename): nb0 = new_notebook(cells=[nbf.v4.new_markdown_cell("""Welcome to the NWB Explorer! -- +This interface allows you to interact with the data in your NWB file both graphically (click on the icons under the 'Controls' columns in the list above) and programmatically. + With this Python console you can programmatically access the loaded data using the [PyNWB Python API](https://pynwb.readthedocs.io/en/stable/). The loaded NWB:N 2 file can be accessed from the variable `nwbfile`. diff --git a/webapp/components/ImageViewer.js b/webapp/components/ImageViewer.js index cef60f5..b28ae59 100644 --- a/webapp/components/ImageViewer.js +++ b/webapp/components/ImageViewer.js @@ -47,13 +47,13 @@ const styles = theme => ({ }, download: { top: "20px", - left: "50px", + left: "40px", opacity: 1.0, position: "absolute" }, play: { top: "20px", - left: "24px", + left: "16px", opacity: 1.0, position: "absolute" } diff --git a/webapp/components/Metadata.js b/webapp/components/Metadata.js index f1ff984..6cd09e7 100644 --- a/webapp/components/Metadata.js +++ b/webapp/components/Metadata.js @@ -57,7 +57,7 @@ export default class Metadata extends React.Component { } else if (variableType.getName() == 'HTML') { metadata = ; } else if (variableType.getName() == 'URL') { - metadata = { variable.getInitialValue().value.url.split('/').slice(-1) }; + metadata = ; } else if (variableType.getChildren && variableType.getChildren()) { metadata = variable.getType().getChildren().filter(v => v.getType().getName() == 'Text').map(v => this.formatField(prettyLabel(v.getId()), this.prettyContent(v.getInitialValue().value.text))); } From c14272b7806e2305d67ab787ac66b384de7cbcf1 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Tue, 25 Feb 2020 13:21:13 -0600 Subject: [PATCH 11/42] typo fix --- nwb_explorer/api.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nwb_explorer/api.py b/nwb_explorer/api.py index 27e8832..1118482 100644 --- a/nwb_explorer/api.py +++ b/nwb_explorer/api.py @@ -29,7 +29,7 @@ def createNotebook(filename): nb0 = new_notebook(cells=[nbf.v4.new_markdown_cell("""Welcome to the NWB Explorer! -- -This interface allows you to interact with the data in your NWB file both graphically (click on the icons under the 'Controls' columns in the list above) and programmatically. +This interface allows you to interact with the data in your NWB file both graphically (click on the icons under the 'Controls' column on the list above) and programmatically. With this Python console you can programmatically access the loaded data using the [PyNWB Python API](https://pynwb.readthedocs.io/en/stable/). From 1412e59a89292ac9b0f9db0a0629a2a1a74b536e Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 26 Feb 2020 11:51:22 +0100 Subject: [PATCH 12/42] #114 fixed download path with no link for local files --- webapp/components/Metadata.js | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/webapp/components/Metadata.js b/webapp/components/Metadata.js index 6cd09e7..898456d 100644 --- a/webapp/components/Metadata.js +++ b/webapp/components/Metadata.js @@ -57,7 +57,12 @@ export default class Metadata extends React.Component { } else if (variableType.getName() == 'HTML') { metadata = ; } else if (variableType.getName() == 'URL') { - metadata = ; + if (variable.getInitialValue().value.url.includes("http")){ + metadata = { variable.getInitialValue().value.url.split('/').slice(-1) } + } else { + metadata = { variable.getInitialValue().value.url.split('//').slice(-1) } + } + } else if (variableType.getChildren && variableType.getChildren()) { metadata = variable.getType().getChildren().filter(v => v.getType().getName() == 'Text').map(v => this.formatField(prettyLabel(v.getId()), this.prettyContent(v.getInitialValue().value.text))); } From 8604872032d4bb20bb24b2f9292655a074694c7b Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 26 Feb 2020 12:09:17 +0100 Subject: [PATCH 13/42] #125 update pillow --- k8s/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/k8s/requirements.txt b/k8s/requirements.txt index d5b335b..d9cf3af 100644 --- a/k8s/requirements.txt +++ b/k8s/requirements.txt @@ -5,4 +5,4 @@ bokeh==0.13.0 holoviews==1.10.6 msgpack-python==0.5.6 nose==1.3.7 -Pillow==5.2.0 \ No newline at end of file +Pillow==6.2.0 \ No newline at end of file From 987007714b9b0942cef4c70479c298587da85ebf Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 26 Feb 2020 12:28:23 +0100 Subject: [PATCH 14/42] #125 back pillow to 5.2.0 --- k8s/requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/k8s/requirements.txt b/k8s/requirements.txt index d9cf3af..d5b335b 100644 --- a/k8s/requirements.txt +++ b/k8s/requirements.txt @@ -5,4 +5,4 @@ bokeh==0.13.0 holoviews==1.10.6 msgpack-python==0.5.6 nose==1.3.7 -Pillow==6.2.0 \ No newline at end of file +Pillow==5.2.0 \ No newline at end of file From 1508e5e6d92ccf55c7aa758f9471d7485da7dfd8 Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Wed, 26 Feb 2020 12:20:10 +0000 Subject: [PATCH 15/42] Two more sample datasets --- webapp/components/FileSampleSelector.js | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) diff --git a/webapp/components/FileSampleSelector.js b/webapp/components/FileSampleSelector.js index b1d4fd7..1225941 100644 --- a/webapp/components/FileSampleSelector.js +++ b/webapp/components/FileSampleSelector.js @@ -10,6 +10,8 @@ const SAMPLE_LINK_FERGUSON_5 = 'https://github.com/OpenSourceBrain/NWBShowcase/r const SAMPLE_LINK_TIMESERIES = 'https://github.com/OpenSourceBrain/NWBShowcase/raw/master/NWB/time_series_data.nwb'; const SAMPLE_LINK_TRIPLETT = 'https://github.com/OpenSourceBrain/NWBShowcase/raw/master/TriplettEtAl2018/TriplettEtAl2018.nwb'; const SAMPLE_LINK_LANTYER = 'https://github.com/OpenSourceBrain/NWBShowcase/raw/master/Lantyer/LantyerEtAl2018.170502_AL_257_CC.nwb'; +const SAMPLE_LINK_LANORE = 'https://github.com/OpenSourceBrain/NWBShowcase/raw/master/IgorPro/141210c3.nwb'; +const SAMPLE_LINK_PACKER = 'https://github.com/OpenSourceBrain/CalciumImagingDriftingGrating/raw/master/neurofinder.01.01.jpg.nwb'; export default class FileSampleSelector extends React.Component { @@ -109,6 +111,24 @@ export default class FileSampleSelector extends React.Component { > Lantyer et al. 2018 +
+ +
+
From 0493fced5edf523147f27be50ac2753f521d0cd7 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 26 Feb 2020 14:49:52 +0100 Subject: [PATCH 16/42] Change image controls color --- webapp/styles/main.less | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/webapp/styles/main.less b/webapp/styles/main.less index df45e2e..54af3f4 100644 --- a/webapp/styles/main.less +++ b/webapp/styles/main.less @@ -576,10 +576,9 @@ iframe{ .imgBtn { font-size: large!important; - color: #07de07!important; + color: @secondary_color; } .imgBtn:hover{ - color: #07de07!important; opacity: 1.0 } From 31e8be28bd264ae84c6d2752b3adcac2a13be816 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 9 Mar 2020 11:10:56 -0700 Subject: [PATCH 17/42] Update pynwb to 1.2.1. Update dependencies pandas, numpy, python-dateutil, h5py, hdmf to match versions in pynwb 1.2.1. Removes outdated imports in mappers file --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 6 +++--- requirements.txt | 12 ++++++------ setup.py | 4 ++-- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 7f317d7..75533ce 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -5,7 +5,7 @@ from pygeppetto.model import Pointer, GenericArray, PointerElement from pynwb import TimeSeries -from pynwb.core import NWBBaseType, ElementIdentifiers, VectorData +from pynwb.core import NWBData from pynwb.core import LabelledDict from pynwb.file import Subject from pynwb.core import DynamicTable @@ -103,7 +103,7 @@ def create_variable(self, name, pynwb_obj, parent_obj): class GenericCompositeMapper(NWBGeppettoMapper): generic = True - excluded_types = (ElementIdentifiers, VectorData) + excluded_types = (NWBData) def __init__(self, model_factory, nwb_geppetto_library): super().__init__(model_factory, nwb_geppetto_library) @@ -272,7 +272,7 @@ def create_variable(self, name, pynwb_obj, parent_obj): class VectorDataMapper(NWBGeppettoMapper): def creates(self, pynwb_obj): - return isinstance(pynwb_obj, VectorData) + return isinstance(pynwb_obj, NWBData) def create_variable(self, name, pynwb_obj, parent_obj): return self.create_variable_base(name, tuple(self.get_value(v) for v in pynwb_obj.data[()])) diff --git a/requirements.txt b/requirements.txt index 93dc126..79f68e2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -14,8 +14,8 @@ defusedxml==0.5.0 Deprecated==1.2.6 entrypoints==0.2.3 filelock==3.0.12 -h5py==2.9.0 -hdmf==1.1.2 +h5py==2.10.0 +hdmf==1.5.4 holoviews==1.10.6 html5lib==1.0.1 idna==2.8 @@ -54,11 +54,11 @@ nbformat==4.4.0 ndx-grayscalevolume==0.0.2 nose==1.3.7 notebook==5.6.0 -numpy==1.15.1 +numpy==1.18.1 nwbwidgets==0.0.2 ordered-set==3.0.1 packaging==19.1 -pandas==0.25.0 +pandas==0.25.3 pandocfilters==1.4.2 param==1.9.1 parso==0.3.1 @@ -77,10 +77,10 @@ pyecore==0.10.2 pygeppetto==0.6.0 Pygments==2.2.0 pymultigen==0.2.0 -pynwb==1.0.3 +pynwb==1.2.1 pyparsing==2.2.0 pyrsistent==0.15.4 -python-dateutil==2.7.3 +python-dateutil==2.8.0 pythreejs==2.1.1 pytz==2018.5 pyviz-comms==0.7.2 diff --git a/setup.py b/setup.py index 2d8d39b..0c0dddf 100644 --- a/setup.py +++ b/setup.py @@ -49,10 +49,10 @@ 'redis==2.10.6', 'seaborn==0.8.1', 'uuid==1.30', - 'pynwb>=1.0.3', + 'pynwb>=1.2.1', 'imageio>=2.5.0', 'quantities>=0.12.3', - 'hdmf==1.1.2', + 'hdmf==1.5.4', 'nwbwidgets==0.0.2' ], ) From 64ac263a58acdc40e890139278eb939c8db79d83 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 9 Mar 2020 15:56:30 -0700 Subject: [PATCH 18/42] Use vectordata and ElementIdentifiers from hdmf.common to replace the ones gone from pynwb.core --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 75533ce..9588f9c 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -5,7 +5,7 @@ from pygeppetto.model import Pointer, GenericArray, PointerElement from pynwb import TimeSeries -from pynwb.core import NWBData +from hdmf.common import ElementIdentifiers, VectorData from pynwb.core import LabelledDict from pynwb.file import Subject from pynwb.core import DynamicTable @@ -103,7 +103,7 @@ def create_variable(self, name, pynwb_obj, parent_obj): class GenericCompositeMapper(NWBGeppettoMapper): generic = True - excluded_types = (NWBData) + excluded_types = (ElementIdentifiers, VectorData) def __init__(self, model_factory, nwb_geppetto_library): super().__init__(model_factory, nwb_geppetto_library) @@ -197,7 +197,7 @@ def get_object_items(self, pynwb_obj): if hasattr(obj_dict, 'items'): items = obj_dict.items() elif is_collection(obj_dict): - items = ((obj_dict[k].name, obj_dict[k]) for k in range(len(obj_dict))) + items = (k if isinstance(obj_dict[k], bool) (obj_dict[k].name, obj_dict[k]) else None for k in range(len(obj_dict))) else: items = () return items @@ -272,7 +272,7 @@ def create_variable(self, name, pynwb_obj, parent_obj): class VectorDataMapper(NWBGeppettoMapper): def creates(self, pynwb_obj): - return isinstance(pynwb_obj, NWBData) + return isinstance(pynwb_obj, VectorData) def create_variable(self, name, pynwb_obj, parent_obj): return self.create_variable_base(name, tuple(self.get_value(v) for v in pynwb_obj.data[()])) From ee38fadf3100f0e43346af019c194c58422e8cff Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 9 Mar 2020 17:05:16 -0700 Subject: [PATCH 19/42] Only add items from collection that have name attribute --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 9588f9c..8af6411 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -18,6 +18,7 @@ from pygeppetto.model.values import Image, Text, ImportValue, StringArray from pygeppetto.model.variables import Variable, TypeToValueMap + nwb_geppetto_mappers = [] @@ -197,11 +198,20 @@ def get_object_items(self, pynwb_obj): if hasattr(obj_dict, 'items'): items = obj_dict.items() elif is_collection(obj_dict): - items = (k if isinstance(obj_dict[k], bool) (obj_dict[k].name, obj_dict[k]) else None for k in range(len(obj_dict))) + items = self.collection_items(obj_dict) else: items = () return items + def collection_items(self, obj_dict): + items=[] + for k in range(len(obj_dict)): + if hasattr(obj_dict[k], "name"): + items.append((obj_dict[k].name, obj_dict[k])) + else: + None + return items; + def sanitize(self, key): return ''.join(k if k.isalnum() else '_' for k in key) From f7f8e74c4f4e262ebaad5098175956884a513246 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 9 Mar 2020 17:06:06 -0700 Subject: [PATCH 20/42] Generate random key as part of notebook path --- webapp/services/NotebookService.js | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/webapp/services/NotebookService.js b/webapp/services/NotebookService.js index 8da5d28..21cfc55 100644 --- a/webapp/services/NotebookService.js +++ b/webapp/services/NotebookService.js @@ -7,7 +7,9 @@ export function getNotebookPath () { if (nwbFileParam){ return "notebook?path=" + nwbFileParam.split('/').slice(-1) + '.ipynb'; } - return "notebook?path=nwbnotebook.ipynb"; + const key = Math.random().toString(36).slice(3); + + return "notebook?path=nwbnotebook" + key + '.ipynb'; } var console = null; From be56a22c974a66471a0ed27c6586d7fb83a673b2 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Tue, 10 Mar 2020 10:55:10 +0100 Subject: [PATCH 21/42] #135 tests fixed --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 2 +- requirements.txt | 2 +- test/test_nwb_data_manager.py | 8 +++++--- 3 files changed, 7 insertions(+), 5 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 8af6411..938de97 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -274,7 +274,7 @@ def creates(cls, value): return is_collection(value) and value and is_metadata(next(iter(value))) def create_variable(self, name, pynwb_obj, parent_obj): - value = StringArray(str(v) for v in pynwb_obj) + value = StringArray(tuple(str(v) for v in pynwb_obj)) array_variable = self.model_factory.create_simple_array_variable(name, value) return array_variable diff --git a/requirements.txt b/requirements.txt index 79f68e2..8c64ffd 100644 --- a/requirements.txt +++ b/requirements.txt @@ -40,7 +40,7 @@ jupyter==1.0.0 jupyter-client==5.2.3 jupyter-console==5.2.0 jupyter-core==4.4.0 -jupyter-geppetto==1.0.0 +jupyter-geppetto==1.0.1 kiwisolver==1.0.1 lxml==4.2.4 MarkupSafe==1.0 diff --git a/test/test_nwb_data_manager.py b/test/test_nwb_data_manager.py index 109fd08..6cd66c4 100644 --- a/test/test_nwb_data_manager.py +++ b/test/test_nwb_data_manager.py @@ -1,10 +1,12 @@ import pytest -from pygeppetto.model.types import ImportType +import os from nwb_explorer.nwb_data_manager import NWBDataManager from pygeppetto.services.model_interpreter import get_model_interpreter +HERE = os.path.dirname(os.path.abspath(__file__)) +ROOT = os.path.dirname(HERE) @pytest.fixture def nwb_data_manager(): @@ -12,11 +14,11 @@ def nwb_data_manager(): def test_get_project_from_url(nwb_data_manager): - fname = 'nwb_files/time_series_data.nwb' + fname = os.path.join(HERE, 'nwb_files/time_series_data.nwb') project = nwb_data_manager.get_project_from_url(fname) assert project.geppettoModel library = project.geppettoModel.variables[0].types[0].eContainer() assert library - assert library.id == 'nwblib' + assert library.id == 'nwbfile' model_interpreter = get_model_interpreter(library.id) assert model_interpreter From 2f109774392dc1163112472cdbeb926881a1cc45 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Tue, 10 Mar 2020 18:27:10 +0100 Subject: [PATCH 22/42] #135 fix console --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 11 +---------- requirements.txt | 2 +- setup.py | 2 +- 3 files changed, 3 insertions(+), 12 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 938de97..bbe4bc5 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -198,20 +198,11 @@ def get_object_items(self, pynwb_obj): if hasattr(obj_dict, 'items'): items = obj_dict.items() elif is_collection(obj_dict): - items = self.collection_items(obj_dict) + items = tuple((obj_dict[k].name, obj_dict[k]) for k in range(len(obj_dict)) if hasattr(obj_dict[k], "name")) else: items = () return items - def collection_items(self, obj_dict): - items=[] - for k in range(len(obj_dict)): - if hasattr(obj_dict[k], "name"): - items.append((obj_dict[k].name, obj_dict[k])) - else: - None - return items; - def sanitize(self, key): return ''.join(k if k.isalnum() else '_' for k in key) diff --git a/requirements.txt b/requirements.txt index 8c64ffd..79f68e2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -40,7 +40,7 @@ jupyter==1.0.0 jupyter-client==5.2.3 jupyter-console==5.2.0 jupyter-core==4.4.0 -jupyter-geppetto==1.0.1 +jupyter-geppetto==1.0.0 kiwisolver==1.0.1 lxml==4.2.4 MarkupSafe==1.0 diff --git a/setup.py b/setup.py index 0c0dddf..81ff07b 100644 --- a/setup.py +++ b/setup.py @@ -53,6 +53,6 @@ 'imageio>=2.5.0', 'quantities>=0.12.3', 'hdmf==1.5.4', - 'nwbwidgets==0.0.2' + 'nwbwidgets>=0.0.2' ], ) From 5251a6dce8d13a0b6f23c414532d272bdd09b2b9 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Tue, 17 Mar 2020 17:04:03 +0100 Subject: [PATCH 23/42] #135 remove reference to jupyter widgets Jupyter widgets aren't working with pynwb v1.2.1 --- nwb_explorer/api.py | 6 ------ 1 file changed, 6 deletions(-) diff --git a/nwb_explorer/api.py b/nwb_explorer/api.py index 1118482..65ffd7b 100644 --- a/nwb_explorer/api.py +++ b/nwb_explorer/api.py @@ -2,15 +2,10 @@ from jupyter_geppetto.webapi import get from notebook.base.handlers import IPythonHandler -from pygeppetto.model.model_serializer import GeppettoModelSerializer from nwb_explorer.nwb_model_interpreter import NWBModelInterpreter -from nwb_explorer.plots_manager import PlotManager -from . import nwb_data_manager from pygeppetto.managers import GeppettoManager -from pygeppetto.managers.geppetto_manager import RuntimeProject -from traitlets import Instance cache_model = False from pygeppetto.services.data_manager import DataManagerHelper @@ -34,7 +29,6 @@ def createNotebook(filename): With this Python console you can programmatically access the loaded data using the [PyNWB Python API](https://pynwb.readthedocs.io/en/stable/). The loaded NWB:N 2 file can be accessed from the variable `nwbfile`. -If you would like to inspect the content of the file using the [NWB Juypyter widgets](https://pypi.org/project/nwbwidgets/) you can use the `show()` function. To execute a command type it and press `Shift+Enter`. To execute a command and create a new cell press `Alt+Enter`."""), nbf.v4.new_code_cell('nwbfile') From 1aa631de4323a08b4842cc4549a36906ab9ccc9a Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 26 Mar 2020 12:02:24 +0000 Subject: [PATCH 24/42] Add silverlab namespaces and allow Nx1x1 D arrays for time series --- .../nwb_model_interpreter/nwb_reader.py | 18 ++++++++-- .../silverlab/silverlab.metadata.yaml | 9 +++++ .../silverlab/silverlab.namespace.yaml | 11 ++++++ .../namespaces/silverlab/silverlab.ophys.yaml | 36 +++++++++++++++++++ 4 files changed, 72 insertions(+), 2 deletions(-) create mode 100644 webapp/namespaces/silverlab/silverlab.metadata.yaml create mode 100644 webapp/namespaces/silverlab/silverlab.namespace.yaml create mode 100644 webapp/namespaces/silverlab/silverlab.ophys.yaml diff --git a/nwb_explorer/nwb_model_interpreter/nwb_reader.py b/nwb_explorer/nwb_model_interpreter/nwb_reader.py index 6c2c0f3..e3ac5cf 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_reader.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_reader.py @@ -8,6 +8,8 @@ from io import BytesIO from PIL import Image as Img import imageio +import numpy as np +import os NWB_ROOT_NAME = 'root' @@ -24,7 +26,10 @@ def get_plottable_timeseries(time_series, resampling_size=None): # TODO we may need to rearrange that when dealing with spatial series: a different type of plot (3D or else) # may me more adequate than what we're doing (i.e. splitting in multiple mono dimensional timeseries) - time_series_array = NWBReader.get_mono_dimensional_timeseries_aux(time_series.data[::1]) + d = time_series.data[::1] + if len(time_series.data.shape)==3 and time_series.data.shape[1]==1 and time_series.data.shape[2]==1: + d = np.array([ b[0][0] for b in time_series.data[::1] ]) + time_series_array = NWBReader.get_mono_dimensional_timeseries_aux(d) return time_series_array @staticmethod @@ -108,7 +113,16 @@ def get_mono_dimensional_timeseries_aux(values): def __init__(self, nwbfile_or_path): if isinstance(nwbfile_or_path, str): - try: + try: + from pynwb import get_class, load_namespaces, NWBHDF5IO + + # This should be temporary. Ideally namespaces should be cached in the NWB files + # See https://github.com/SilverLabUCL/PySilverLabNWB/issues/26 + namespace_dir = 'webapp/namespaces' + namespace_file = os.path.join(namespace_dir, 'silverlab/silverlab.namespace.yaml') + load_namespaces(namespace_file) + get_class('ZplanePockelsDataset', 'silverlab_extended_schema') + io = NWBHDF5IO(nwbfile_or_path, 'r') nwbfile = io.read() except Exception as e: diff --git a/webapp/namespaces/silverlab/silverlab.metadata.yaml b/webapp/namespaces/silverlab/silverlab.metadata.yaml new file mode 100644 index 0000000..ee6acf1 --- /dev/null +++ b/webapp/namespaces/silverlab/silverlab.metadata.yaml @@ -0,0 +1,9 @@ +groups: +- neurodata_type_def: SilverLabMetaData + neurodata_type_inc: LabMetaData + doc: A place to store Silver lab specific metadata + attributes: + - name: silverlab_api_version + dtype: text + doc: For potential future backwards compatibility, store the 'version' of this + API that created the file. diff --git a/webapp/namespaces/silverlab/silverlab.namespace.yaml b/webapp/namespaces/silverlab/silverlab.namespace.yaml new file mode 100644 index 0000000..2787713 --- /dev/null +++ b/webapp/namespaces/silverlab/silverlab.namespace.yaml @@ -0,0 +1,11 @@ +namespaces: +- doc: Extensions for acousto-optic lens data + full_name: Silver lab data extension to NWB format for acousto-optic lens experiments + name: silverlab_extended_schema + schema: + - namespace: core + neurodata_types: + - LabMetaData + - source: silverlab.ophys.yaml + - source: silverlab.metadata.yaml + version: '0.2' diff --git a/webapp/namespaces/silverlab/silverlab.ophys.yaml b/webapp/namespaces/silverlab/silverlab.ophys.yaml new file mode 100644 index 0000000..3fdf48c --- /dev/null +++ b/webapp/namespaces/silverlab/silverlab.ophys.yaml @@ -0,0 +1,36 @@ +groups: +- neurodata_type_def: SilverLabOptophysiology + neurodata_type_inc: LabMetaData + doc: A place to store Silver lab specific optophysiology data + attributes: + - name: cycle_time + dtype: float + doc: time in seconds for the microscope to acquire all ROIs once and return to + its starting position + - name: cycles_per_trial + dtype: int + doc: how many microscope cycles occur in each experimental trial + - name: frame_size + dtype: int + shape: + - 2 + doc: the 2d imaging frame size in voxels + - name: imaging_mode + dtype: text + doc: the acquisition mode for the experiment; pointing = single-voxel ROIs, miniscan + = 2d rectangular ROIs, volume = 3d cuboid ROIs + datasets: + - neurodata_type_def: ZplanePockelsDataset + name: pockels + shape: + - null + - 4 + doc: "pockels data set, recording calibration data for focusing at different z-planes\ + \ in four columns: Z offset from focal plane (micrometres), normalised Z, 'Pockels'\ + \ i.e. laser power in %, and z offset for drive motors" + attributes: + - name: columns + dtype: text + shape: + - 4 + doc: column names for the zplane pockels dataset From ac91b7bf8389c5e4ab87cb8d125766dca6ca594f Mon Sep 17 00:00:00 2001 From: Padraig Gleeson Date: Thu, 26 Mar 2020 12:23:50 +0000 Subject: [PATCH 25/42] Optimisation --- nwb_explorer/nwb_model_interpreter/nwb_reader.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_reader.py b/nwb_explorer/nwb_model_interpreter/nwb_reader.py index e3ac5cf..1a026d4 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_reader.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_reader.py @@ -28,7 +28,7 @@ def get_plottable_timeseries(time_series, resampling_size=None): # may me more adequate than what we're doing (i.e. splitting in multiple mono dimensional timeseries) d = time_series.data[::1] if len(time_series.data.shape)==3 and time_series.data.shape[1]==1 and time_series.data.shape[2]==1: - d = np.array([ b[0][0] for b in time_series.data[::1] ]) + d = d.reshape(time_series.data.shape[0]) time_series_array = NWBReader.get_mono_dimensional_timeseries_aux(d) return time_series_array From 140f0829676dac99fad12993084fefd2d46c8c9a Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 1 Apr 2020 17:31:02 +0200 Subject: [PATCH 26/42] #149 Generalized approach to extensions --- .../silverlab/silverlab.metadata.yaml | 0 .../silverlab/silverlab.namespace.yaml | 0 .../silverlab/silverlab.ophys.yaml | 0 .../nwb_model_interpreter/nwb_reader.py | 34 +++++------- webapp/package-lock.json | 54 ++++++++++++------- 5 files changed, 49 insertions(+), 39 deletions(-) rename {webapp/namespaces => nwb-extensions}/silverlab/silverlab.metadata.yaml (100%) rename {webapp/namespaces => nwb-extensions}/silverlab/silverlab.namespace.yaml (100%) rename {webapp/namespaces => nwb-extensions}/silverlab/silverlab.ophys.yaml (100%) diff --git a/webapp/namespaces/silverlab/silverlab.metadata.yaml b/nwb-extensions/silverlab/silverlab.metadata.yaml similarity index 100% rename from webapp/namespaces/silverlab/silverlab.metadata.yaml rename to nwb-extensions/silverlab/silverlab.metadata.yaml diff --git a/webapp/namespaces/silverlab/silverlab.namespace.yaml b/nwb-extensions/silverlab/silverlab.namespace.yaml similarity index 100% rename from webapp/namespaces/silverlab/silverlab.namespace.yaml rename to nwb-extensions/silverlab/silverlab.namespace.yaml diff --git a/webapp/namespaces/silverlab/silverlab.ophys.yaml b/nwb-extensions/silverlab/silverlab.ophys.yaml similarity index 100% rename from webapp/namespaces/silverlab/silverlab.ophys.yaml rename to nwb-extensions/silverlab/silverlab.ophys.yaml diff --git a/nwb_explorer/nwb_model_interpreter/nwb_reader.py b/nwb_explorer/nwb_model_interpreter/nwb_reader.py index 1a026d4..1389bdf 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_reader.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_reader.py @@ -10,8 +10,10 @@ import imageio import numpy as np import os -NWB_ROOT_NAME = 'root' +import glob +NWB_ROOT_NAME = 'root' +EXTENSION_PATH = 'nwb-extensions' class NWBReader: nwb_map_id_api = {'acquisition': 'acquisition', @@ -23,11 +25,10 @@ class NWBReader: @staticmethod def get_plottable_timeseries(time_series, resampling_size=None): - # TODO we may need to rearrange that when dealing with spatial series: a different type of plot (3D or else) # may me more adequate than what we're doing (i.e. splitting in multiple mono dimensional timeseries) d = time_series.data[::1] - if len(time_series.data.shape)==3 and time_series.data.shape[1]==1 and time_series.data.shape[2]==1: + if len(time_series.data.shape) == 3 and time_series.data.shape[1] == 1 and time_series.data.shape[2] == 1: d = d.reshape(time_series.data.shape[0]) time_series_array = NWBReader.get_mono_dimensional_timeseries_aux(d) return time_series_array @@ -107,22 +108,17 @@ def get_mono_dimensional_timeseries_aux(values): # def get_timeseries_dimensions(time_series): # return 1 if len(time_series.data.shape) == 1 else time_series.data.shape[0] - - - - def __init__(self, nwbfile_or_path): if isinstance(nwbfile_or_path, str): - try: + try: from pynwb import get_class, load_namespaces, NWBHDF5IO - + # This should be temporary. Ideally namespaces should be cached in the NWB files # See https://github.com/SilverLabUCL/PySilverLabNWB/issues/26 - namespace_dir = 'webapp/namespaces' - namespace_file = os.path.join(namespace_dir, 'silverlab/silverlab.namespace.yaml') - load_namespaces(namespace_file) - get_class('ZplanePockelsDataset', 'silverlab_extended_schema') - + for namespace_file in glob.glob(EXTENSION_PATH + '/**/*.namespace.*ml'): + load_namespaces(namespace_file) + # get_class('ZplanePockelsDataset', 'silverlab_extended_schema') + io = NWBHDF5IO(nwbfile_or_path, 'r') nwbfile = io.read() except Exception as e: @@ -133,7 +129,6 @@ def __init__(self, nwbfile_or_path): self.__data_interfaces = None self.__time_series_list = None - def retrieve_from_path(self, path_pieces): '''Finds paths as extracted by `extract_time_series_path`''' @@ -154,7 +149,6 @@ def retrieve_from_path(self, path_pieces): # path = NWBReader.find_from_key_recursive(self.nwbfile.fields, time_series) # return path - def get_data_interfaces(self): if not self.__data_interfaces: self.__data_interfaces = self._get_data_interfaces(self.nwbfile) @@ -182,7 +176,6 @@ def _get_data_interfaces(self, node): # self.__time_series_list = self._get_timeseries() # return self.__time_series_list - def get_nwbfile(self): return self.nwbfile @@ -267,7 +260,6 @@ def _check_requirement_data_interfaces(self, requirement): # def get_all(self): # return self.nwbfile.all_children() - # @staticmethod # def img_to_base64(plottable_image): # img = Img.fromarray(plottable_image, 'RGB') @@ -284,7 +276,7 @@ def img_to_string(plottable_image): output = BytesIO() img.save(output, format='PNG') output.seek(0, 0) - + return output.getvalue() def get_image(self, name: str, interface: str, index: str) -> base64: @@ -305,7 +297,7 @@ def get_image(self, name: str, interface: str, index: str) -> base64: np_image = pynwb_obj.data[()] if len(np_image.shape) > 3: np_image = np_image[index] - + return NWBReader.img_to_string(np_image) - return None \ No newline at end of file + return None diff --git a/webapp/package-lock.json b/webapp/package-lock.json index 2e77217..a390b1f 100644 --- a/webapp/package-lock.json +++ b/webapp/package-lock.json @@ -892,7 +892,6 @@ "file-loader": "^2.0.0", "file-saver": "^1.3.3", "google-maps": "^3.2.1", - "griddle-0.6-fork": "git+https://github.com/rodriguez-facundo/griddle.git#218468b8c438295f8b3c6a8229491eb7972ed85e", "griddle-react": "^1.13.1", "handlebars": "^4.0.5", "html2canvas": "^1.0.0-alpha.12", @@ -943,6 +942,16 @@ "underscore": "^1.8.3", "url-join": "^4.0.0", "velocity.java": "^1.3.1" + }, + "dependencies": { + "griddle-0.6-fork": { + "version": "git+https://github.com/rodriguez-facundo/griddle.git#218468b8c438295f8b3c6a8229491eb7972ed85e", + "from": "git+https://github.com/rodriguez-facundo/griddle.git#218468b8c438295f8b3c6a8229491eb7972ed85e", + "requires": { + "lodash": "^4.12.0", + "prop-types": "^15.6.2" + } + } } }, "@icons/material": { @@ -9696,14 +9705,6 @@ "resolved": "https://registry.npmjs.org/grid-index/-/grid-index-1.1.0.tgz", "integrity": "sha512-HZRwumpOGUrHyxO5bqKZL0B0GlUpwtCAzZ42sgxUPniu33R1LSFH5yrIcBCHjkctCAh3mtWKcKd9J4vDDdeVHA==" }, - "griddle-0.6-fork": { - "version": "git+https://github.com/rodriguez-facundo/griddle.git#218468b8c438295f8b3c6a8229491eb7972ed85e", - "from": "git+https://github.com/rodriguez-facundo/griddle.git", - "requires": { - "lodash": "^4.12.0", - "prop-types": "^15.6.2" - } - }, "griddle-react": { "version": "1.13.1", "resolved": "https://registry.npmjs.org/griddle-react/-/griddle-react-1.13.1.tgz", @@ -21094,7 +21095,8 @@ }, "ansi-regex": { "version": "2.1.1", - "bundled": true + "bundled": true, + "optional": true }, "aproba": { "version": "1.2.0", @@ -21131,7 +21133,8 @@ }, "code-point-at": { "version": "1.1.0", - "bundled": true + "bundled": true, + "optional": true }, "concat-map": { "version": "0.0.1", @@ -21140,7 +21143,8 @@ }, "console-control-strings": { "version": "1.1.0", - "bundled": true + "bundled": true, + "optional": true }, "core-util-is": { "version": "1.0.2", @@ -21243,7 +21247,8 @@ }, "inherits": { "version": "2.0.3", - "bundled": true + "bundled": true, + "optional": true }, "ini": { "version": "1.3.5", @@ -21253,6 +21258,7 @@ "is-fullwidth-code-point": { "version": "1.0.0", "bundled": true, + "optional": true, "requires": { "number-is-nan": "^1.0.0" } @@ -21278,6 +21284,7 @@ "minipass": { "version": "2.3.5", "bundled": true, + "optional": true, "requires": { "safe-buffer": "^5.1.2", "yallist": "^3.0.0" @@ -21294,6 +21301,7 @@ "mkdirp": { "version": "0.5.1", "bundled": true, + "optional": true, "requires": { "minimist": "0.0.8" } @@ -21377,6 +21385,7 @@ "once": { "version": "1.4.0", "bundled": true, + "optional": true, "requires": { "wrappy": "1" } @@ -21452,7 +21461,8 @@ }, "safe-buffer": { "version": "5.1.2", - "bundled": true + "bundled": true, + "optional": true }, "safer-buffer": { "version": "2.1.2", @@ -21482,6 +21492,7 @@ "string-width": { "version": "1.0.2", "bundled": true, + "optional": true, "requires": { "code-point-at": "^1.0.0", "is-fullwidth-code-point": "^1.0.0", @@ -21499,6 +21510,7 @@ "strip-ansi": { "version": "3.0.1", "bundled": true, + "optional": true, "requires": { "ansi-regex": "^2.0.0" } @@ -21537,11 +21549,13 @@ }, "wrappy": { "version": "1.0.2", - "bundled": true + "bundled": true, + "optional": true }, "yallist": { "version": "3.0.3", - "bundled": true + "bundled": true, + "optional": true } } }, @@ -22547,6 +22561,7 @@ "version": "2.3.5", "bundled": true, "dev": true, + "optional": true, "requires": { "safe-buffer": "^5.1.2", "yallist": "^3.0.0" @@ -22565,6 +22580,7 @@ "version": "0.5.1", "bundled": true, "dev": true, + "optional": true, "requires": { "minimist": "0.0.8" } @@ -22744,7 +22760,8 @@ "safe-buffer": { "version": "5.1.2", "bundled": true, - "dev": true + "dev": true, + "optional": true }, "safer-buffer": { "version": "2.1.2", @@ -22850,7 +22867,8 @@ "yallist": { "version": "3.0.3", "bundled": true, - "dev": true + "dev": true, + "optional": true } } }, From 717a1a80787ffac6df959fa05092085fa3c7990d Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 1 Apr 2020 18:05:17 +0200 Subject: [PATCH 27/42] #149 Fixed npm compilation ts issue --- webapp/package-lock.json | 4484 +++++++++++++++++++++----------------- webapp/package.json | 2 +- webapp/tsconfig.json | 36 +- 3 files changed, 2495 insertions(+), 2027 deletions(-) diff --git a/webapp/package-lock.json b/webapp/package-lock.json index a390b1f..38b68aa 100644 --- a/webapp/package-lock.json +++ b/webapp/package-lock.json @@ -15,28 +15,40 @@ } }, "@babel/code-frame": { - "version": "7.5.5", - "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.5.5.tgz", - "integrity": "sha512-27d4lZoomVyo51VegxI20xZPuSHusqbQag/ztrBC7wegWoQ1nLREPVSKSW8byhTlzTKyNE4ifaTA6lCp7JjpFw==", + "version": "7.8.3", + "resolved": "https://registry.npmjs.org/@babel/code-frame/-/code-frame-7.8.3.tgz", + "integrity": "sha512-a9gxpmdXtZEInkCSHUJDLHZVBgb1QS0jhss4cPP93EW7s+uC5bikET2twEF3KV+7rDblJcmNvTR7VJejqd2C2g==", "requires": { - 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"chokidar": "^2.1.6", + "chokidar": "^2.1.8", "compression": "^1.7.4", "connect-history-api-fallback": "^1.6.0", "debug": "^4.1.1", "del": "^4.1.1", "express": "^4.17.1", "html-entities": "^1.2.1", - "http-proxy-middleware": "^0.19.1", + "http-proxy-middleware": "0.19.1", "import-local": "^2.0.0", "internal-ip": "^4.3.0", "ip": "^1.1.5", - "is-absolute-url": "^3.0.0", + "is-absolute-url": "^3.0.3", "killable": "^1.0.1", - "loglevel": "^1.6.3", + "loglevel": "^1.6.6", "opn": "^5.5.0", "p-retry": "^3.0.1", - "portfinder": "^1.0.21", + "portfinder": "^1.0.25", "schema-utils": "^1.0.0", - "selfsigned": "^1.10.4", + "selfsigned": "^1.10.7", "semver": "^6.3.0", "serve-index": "^1.9.1", "sockjs": "0.3.19", - "sockjs-client": "1.3.0", + "sockjs-client": "1.4.0", "spdy": "^4.0.1", "strip-ansi": "^3.0.1", "supports-color": "^6.1.0", "url": "^0.11.0", - "webpack-dev-middleware": "^3.7.0", + "webpack-dev-middleware": "^3.7.2", "webpack-log": "^2.0.0", "ws": "^6.2.1", "yargs": "12.0.5" @@ -22293,9 +22690,9 @@ } }, "faye-websocket": { - 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"node-pre-gyp": "^0.12.0" + "node-pre-gyp": "*" }, "dependencies": { "abbrev": { @@ -22380,7 +22786,7 @@ } }, "chownr": { - "version": "1.1.1", + "version": "1.1.4", "bundled": true, "dev": true, "optional": true @@ -22410,7 +22816,7 @@ "optional": true }, "debug": { - "version": "4.1.1", + "version": "3.2.6", "bundled": true, "dev": true, "optional": true, @@ -22437,12 +22843,12 @@ "optional": true }, "fs-minipass": { - "version": "1.2.5", + "version": "1.2.7", "bundled": true, "dev": true, "optional": true, "requires": { - "minipass": "^2.2.1" + "minipass": "^2.6.0" } }, "fs.realpath": { @@ -22468,7 +22874,7 @@ } }, "glob": { - "version": "7.1.3", + "version": "7.1.6", "bundled": true, "dev": true, "optional": true, @@ -22497,7 +22903,7 @@ } }, "ignore-walk": { - "version": "3.0.1", + "version": "3.0.3", "bundled": true, "dev": true, "optional": true, @@ -22516,7 +22922,7 @@ } }, "inherits": { - "version": "2.0.3", + "version": "2.0.4", "bundled": true, "dev": true, "optional": true @@ -22552,13 +22958,13 @@ } }, "minimist": { - "version": "0.0.8", + "version": "1.2.5", "bundled": true, "dev": true, "optional": true }, "minipass": { - "version": "2.3.5", + "version": "2.9.0", "bundled": true, "dev": true, "optional": true, @@ -22568,42 +22974,42 @@ } }, "minizlib": { - "version": "1.2.1", + "version": "1.3.3", "bundled": true, "dev": true, "optional": true, "requires": { - "minipass": "^2.2.1" + "minipass": "^2.9.0" } }, "mkdirp": { - "version": "0.5.1", + "version": "0.5.3", "bundled": true, "dev": true, "optional": true, "requires": { - "minimist": "0.0.8" + "minimist": "^1.2.5" } }, "ms": { - "version": "2.1.1", + "version": "2.1.2", "bundled": true, "dev": true, "optional": true }, "needle": { - "version": "2.3.0", + "version": "2.3.3", "bundled": true, "dev": true, "optional": true, "requires": { - "debug": "^4.1.0", + "debug": "^3.2.6", "iconv-lite": "^0.4.4", "sax": "^1.2.4" } }, "node-pre-gyp": { - "version": "0.12.0", + "version": "0.14.0", "bundled": true, "dev": true, "optional": true, @@ -22617,11 +23023,11 @@ "rc": "^1.2.7", "rimraf": "^2.6.1", "semver": "^5.3.0", - "tar": "^4" + "tar": "^4.4.2" } }, "nopt": { - "version": "4.0.1", + "version": "4.0.3", "bundled": true, "dev": true, "optional": true, @@ -22631,19 +23037,29 @@ } }, "npm-bundled": { - "version": "1.0.6", + "version": "1.1.1", + "bundled": true, + "dev": true, + "optional": true, + "requires": { + "npm-normalize-package-bin": "^1.0.1" + } + }, + "npm-normalize-package-bin": { + "version": "1.0.1", "bundled": true, "dev": true, "optional": true }, "npm-packlist": { - "version": "1.4.1", + "version": "1.4.8", "bundled": true, "dev": true, "optional": true, "requires": { "ignore-walk": "^3.0.1", - "npm-bundled": "^1.0.1" + "npm-bundled": "^1.0.1", + "npm-normalize-package-bin": "^1.0.1" } }, "npmlog": { @@ -22708,7 +23124,7 @@ "optional": true }, "process-nextick-args": { - "version": "2.0.0", + "version": "2.0.1", "bundled": true, "dev": true, "optional": true @@ -22723,18 +23139,10 @@ "ini": "~1.3.0", "minimist": "^1.2.0", "strip-json-comments": "~2.0.1" - }, - "dependencies": { - "minimist": { - "version": "1.2.0", - "bundled": true, - "dev": true, - "optional": true - } } }, "readable-stream": { - "version": "2.3.6", + "version": "2.3.7", "bundled": true, "dev": true, "optional": true, @@ -22749,7 +23157,7 @@ } }, "rimraf": { - "version": "2.6.3", + "version": "2.7.1", "bundled": true, "dev": true, "optional": true, @@ -22776,7 +23184,7 @@ "optional": true }, "semver": { - "version": "5.7.0", + "version": "5.7.1", "bundled": true, "dev": true, "optional": true @@ -22829,18 +23237,18 @@ "optional": true }, "tar": { - "version": "4.4.8", + "version": "4.4.13", "bundled": true, "dev": true, "optional": true, "requires": { "chownr": "^1.1.1", "fs-minipass": "^1.2.5", - "minipass": "^2.3.4", - "minizlib": "^1.1.1", + "minipass": "^2.8.6", + "minizlib": "^1.2.1", "mkdirp": "^0.5.0", "safe-buffer": "^5.1.2", - "yallist": "^3.0.2" + "yallist": "^3.0.3" } }, "util-deprecate": { @@ -22865,7 +23273,7 @@ "optional": true }, "yallist": { - "version": "3.0.3", + "version": "3.1.1", "bundled": true, "dev": true, "optional": true @@ -22918,9 +23326,9 @@ "dev": true }, "is-absolute-url": { - 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"version": "1.3.0", - "resolved": "https://registry.npmjs.org/sockjs-client/-/sockjs-client-1.3.0.tgz", - "integrity": "sha512-R9jxEzhnnrdxLCNln0xg5uGHqMnkhPSTzUZH2eXcR03S/On9Yvoq2wyUZILRUhZCNVu2PmwWVoyuiPz8th8zbg==", + "version": "1.4.0", + "resolved": "https://registry.npmjs.org/sockjs-client/-/sockjs-client-1.4.0.tgz", + "integrity": "sha512-5zaLyO8/nri5cua0VtOrFXBPK1jbL4+1cebT/mmKA1E1ZXOvJrII75bPu0l0k843G/+iAbhEqzyKr0w/eCCj7g==", "dev": true, "requires": { "debug": "^3.2.5", @@ -23091,6 +23543,15 @@ "ms": "^2.1.1" } }, + "faye-websocket": { + "version": "0.11.3", + "resolved": "https://registry.npmjs.org/faye-websocket/-/faye-websocket-0.11.3.tgz", + "integrity": "sha512-D2y4bovYpzziGgbHYtGCMjlJM36vAl/y+xUyn1C+FVx8szd1E+86KwVw6XvYSzOP8iMpm1X0I4xJD+QtUb36OA==", + "dev": true, + "requires": { + "websocket-driver": ">=0.5.1" + } + }, "ms": { "version": "2.1.2", "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz", @@ -23130,9 +23591,9 @@ } }, "webpack-dev-middleware": { - "version": "3.7.1", - "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-3.7.1.tgz", - "integrity": "sha512-5MWu9SH1z3hY7oHOV6Kbkz5x7hXbxK56mGHNqHTe6d+ewxOwKUxoUJBs7QIaJb33lPjl9bJZ3X0vCoooUzC36A==", + "version": "3.7.2", + "resolved": "https://registry.npmjs.org/webpack-dev-middleware/-/webpack-dev-middleware-3.7.2.tgz", + "integrity": "sha512-1xC42LxbYoqLNAhV6YzTYacicgMZQTqRd27Sim9wn5hJrX3I5nxYy1SxSd4+gjUFsz1dQFj+yEe6zEVmSkeJjw==", "dev": true, "requires": { "memory-fs": "^0.4.1", @@ -23308,6 +23769,11 @@ "resolved": "https://registry.npmjs.org/window-size/-/window-size-0.1.0.tgz", "integrity": "sha1-VDjNLqk7IC76Ohn+iIeu58lPnJ0=" }, + "word-wrap": { + "version": "1.2.3", + "resolved": "https://registry.npmjs.org/word-wrap/-/word-wrap-1.2.3.tgz", + "integrity": "sha512-Hz/mrNwitNRh/HUAtM/VT/5VH+ygD6DV7mYKZAtHOrbs8U7lvPS6xf7EJKMF0uW1KJCl0H701g3ZGus+muE5vQ==" + }, "wordwrap": { "version": "0.0.3", "resolved": "https://registry.npmjs.org/wordwrap/-/wordwrap-0.0.3.tgz", diff --git a/webapp/package.json b/webapp/package.json index 3ab672a..3aee6dc 100644 --- a/webapp/package.json +++ b/webapp/package.json @@ -48,7 +48,7 @@ "@types/material-ui": "^0.21.5", "@types/react": "^16.4.9", "@types/react-dom": "^16.0.7", - "awesome-typescript-loader": "^5.0.0-1", + "awesome-typescript-loader": "^5.2.1", "babel-eslint": "^10.0.1", "babel-plugin-transform-decorators-legacy": "^1.3.5", "babel-plugin-transform-object-assign": "^6.8.0", diff --git a/webapp/tsconfig.json b/webapp/tsconfig.json index 407ebd0..d731647 100755 --- a/webapp/tsconfig.json +++ b/webapp/tsconfig.json @@ -1,19 +1,21 @@ { - "compilerOptions": { - "outDir": "./dist/", - "sourceMap": true, - "noImplicitAny": true, - "module": "commonjs", - "target": "es5", - "stripInternal":true, - "alwaysStrict":true, - "forceConsistentCasingInFileNames": true, - "noImplicitReturns": true, - "strict": true, - "noUnusedLocals": true, - "jsx": "react" - }, - "include": [ - "./node_modules/@geppettoengine/geppetto-client/js/components/interface/flexLayout2/src/**/*", "./@geppettoengine/geppetto-client/js/components/interface/flexLayout2/examples/demo/*" - ] + "compilerOptions": { + "outDir": "./dist/", + "sourceMap": true, + "noImplicitAny": true, + "module": "commonjs", + "target": "es5", + "stripInternal": true, + "alwaysStrict": true, + "forceConsistentCasingInFileNames": true, + "noImplicitReturns": true, + "strict": true, + "noUnusedLocals": true, + "jsx": "react", + "lib": ["dom", "es2015"] + }, + "include": [ + "./node_modules/@geppettoengine/geppetto-client/js/components/interface/flexLayout2/src/**/*", + "./@geppettoengine/geppetto-client/js/components/interface/flexLayout2/examples/demo/*" + ] } From 807e149cfdf292619ab35031665b9e2cc6827279 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 1 Apr 2020 18:40:26 +0200 Subject: [PATCH 28/42] #149 Fixed file loading with extension. Tested --- nwb-extensions/README.md | 3 +++ nwb-extensions/silverlab/init.py | 1 + nwb_explorer/__init__.py | 27 +++++++++++++++++++ .../nwb_model_interpreter/nwb_reader.py | 17 +++--------- 4 files changed, 35 insertions(+), 13 deletions(-) create mode 100644 nwb-extensions/README.md create mode 100644 nwb-extensions/silverlab/init.py diff --git a/nwb-extensions/README.md b/nwb-extensions/README.md new file mode 100644 index 0000000..2706dd3 --- /dev/null +++ b/nwb-extensions/README.md @@ -0,0 +1,3 @@ +# Custom pynwb extensions + +Place your extensions here \ No newline at end of file diff --git a/nwb-extensions/silverlab/init.py b/nwb-extensions/silverlab/init.py new file mode 100644 index 0000000..35ecf54 --- /dev/null +++ b/nwb-extensions/silverlab/init.py @@ -0,0 +1 @@ +pynwb.get_class('ZplanePockelsDataset', 'silverlab_extended_schema') \ No newline at end of file diff --git a/nwb_explorer/__init__.py b/nwb_explorer/__init__.py index 8753a2e..fb97266 100644 --- a/nwb_explorer/__init__.py +++ b/nwb_explorer/__init__.py @@ -1,4 +1,8 @@ import logging +import glob +import os +import pynwb +from pynwb import load_namespaces from jupyter_geppetto.webapi import RouteManager from pygeppetto.services import model_interpreter, data_manager @@ -7,6 +11,8 @@ from nwb_explorer.nwb_data_manager import NWBDataManager from nwb_explorer.nwb_model_interpreter import NWBModelInterpreter +EXTENSION_PATH = 'nwb-extensions' + # Add REST API RouteManager.add_controller(api.NWBController) logging.info("Adding NWBModelInterpreter") @@ -16,3 +22,24 @@ logging.info("Adding NWBDataManager") # Replace data manager data_manager.set_data_manager(NWBDataManager()) + + +# This should be temporary. Ideally namespaces should be cached in the NWB files +# See https://github.com/SilverLabUCL/PySilverLabNWB/issues/26 +def init_extensions(): + + for namespace_file in glob.glob(EXTENSION_PATH + '/**/*.namespace.*ml'): + extension_path = os.path.dirname(namespace_file) + extension_name = os.path.basename(extension_path) + logging.info('Initializing extension ' + extension_name) + load_namespaces(namespace_file) + + init_file = os.path.join(extension_path, 'init.py') + if os.path.exists(init_file): + try: + with open(init_file) as f: + for line in f: + eval(line) + except Exception as e: + logging.error("Error evaluating extension init file " + init_file, exc_info=True) +init_extensions() \ No newline at end of file diff --git a/nwb_explorer/nwb_model_interpreter/nwb_reader.py b/nwb_explorer/nwb_model_interpreter/nwb_reader.py index 1389bdf..afc713f 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_reader.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_reader.py @@ -1,7 +1,4 @@ -import collections - -import numpy as np -from pynwb import TimeSeries, NWBHDF5IO, ProcessingModule +from pynwb import NWBHDF5IO from pynwb.core import NWBDataInterface from pynwb.image import ImageSeries import base64 @@ -9,11 +6,11 @@ from PIL import Image as Img import imageio import numpy as np -import os -import glob + + NWB_ROOT_NAME = 'root' -EXTENSION_PATH = 'nwb-extensions' + class NWBReader: nwb_map_id_api = {'acquisition': 'acquisition', @@ -111,13 +108,7 @@ def get_mono_dimensional_timeseries_aux(values): def __init__(self, nwbfile_or_path): if isinstance(nwbfile_or_path, str): try: - from pynwb import get_class, load_namespaces, NWBHDF5IO - # This should be temporary. Ideally namespaces should be cached in the NWB files - # See https://github.com/SilverLabUCL/PySilverLabNWB/issues/26 - for namespace_file in glob.glob(EXTENSION_PATH + '/**/*.namespace.*ml'): - load_namespaces(namespace_file) - # get_class('ZplanePockelsDataset', 'silverlab_extended_schema') io = NWBHDF5IO(nwbfile_or_path, 'r') nwbfile = io.read() From 8c70ced4bc4aa7a912daf3efc204f8d34ce5044e Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 8 Apr 2020 12:39:03 +0200 Subject: [PATCH 29/42] #145 Fixed bug on add plots --- webapp/components/AddPlotMenu.js | 155 +++++++++--------- .../reduxconnect/AddPlotMenuConnect.js | 4 +- webapp/middleware/nwbMiddleware.js | 2 +- 3 files changed, 82 insertions(+), 79 deletions(-) diff --git a/webapp/components/AddPlotMenu.js b/webapp/components/AddPlotMenu.js index 66dcdc3..6fc2d5c 100644 --- a/webapp/components/AddPlotMenu.js +++ b/webapp/components/AddPlotMenu.js @@ -1,104 +1,107 @@ -import React, { Component } from 'react' -import Icon from '@material-ui/core/Icon'; -import Popover from '@material-ui/core/Popover'; -import MenuItem from '@material-ui/core/MenuItem'; -import { CompactPicker } from 'react-color'; +import React, { Component } from "react"; +import Menu from "@material-ui/core/Menu"; +import Popover from "@material-ui/core/Popover"; +import MenuItem from "@material-ui/core/MenuItem"; +import { CompactPicker } from "react-color"; const anchor = { origin: { - vertical: 'bottom', - horizontal: 'right', + vertical: "bottom", + horizontal: "right", }, transform: { - vertical: 'top', - horizontal: 'right', - } -} + vertical: "top", + horizontal: "right", + }, +}; export default class AddPlotMenu extends Component { state = { anchorEl: null, - hostId: null - } + selectedPlot: null, + }; - goOnlyToTimeseriesWidgets = this.goOnlyToTimeseriesWidgets.bind(this) - dontGoToSameHostTwice = this.dontGoToSameHostTwice.bind(this) + goOnlyToTimeseriesWidgets = this.goOnlyToTimeseriesWidgets.bind(this); + dontGoToSameHostTwice = this.dontGoToSameHostTwice.bind(this); clickAddToWidget (color) { - const { hostId } = this.state - const { instancePath, action } = this.props - action({ hostId, instancePath, color: color.hex, type: "timeseries" }) - this.setState({ anchorEl: null, hostId: null }) + const { selectedPlot } = this.state; + const { instancePath, action } = this.props; + action({ + hostId: selectedPlot.id, + instancePath, + color: color.hex, + type: "timeseries", + }); + this.setState({ anchorEl: null, selectedPlot: null }); } dontGoToSameHostTwice (widget) { - const { guestList } = widget + const { guestList } = widget; if (guestList) { - const list = guestList.map(guest => guest.instancePath) - return list.indexOf(this.props.instancePath) == -1 + const list = guestList.map(guest => guest.instancePath); + return list.indexOf(this.props.instancePath) == -1; } - return true + return true; } goOnlyToTimeseriesWidgets (widget) { - const { instancePath } = this.props - return widget.component == 'Plot' && widget.instancePath != instancePath + const { instancePath } = this.props; + return widget.instancePath != instancePath; } render () { - const { anchorEl, hostId, color } = this.state; - const { widgets, icon, instancePath } = this.props - let popover = [] + const { anchorEl, selectedPlot, color } = this.state; + const { widgets, icon, instancePath } = this.props; - const hostIds = Object.values(widgets) + const availablePlots = widgets .filter(this.goOnlyToTimeseriesWidgets) - .filter(this.dontGoToSameHostTwice) - .map(widget => widget.id) - - if (anchorEl) { - popover = ( - this.setState({ anchorEl: null })} - transformOrigin={anchor.transform} - > - {hostId - ? this.clickAddToWidget(color)} - /> - : hostIds.map(hostId => - this.setState({ hostId })} - > - { widgets[hostId].name } - - )} - - - ) + .filter(this.dontGoToSameHostTwice); + if (!availablePlots.length) { + return ''; } - if (hostIds.length){ - return ( - hostIds.length > 0 ? this.setState({ anchorEl: e.currentTarget }) : {}}> - - { popover } - - ) - } - return ''; - + return + + availablePlots.length > 0 + ? this.setState({ anchorEl: e.currentTarget }) + : {} + } + > + {" "} + + + this.setState({ anchorEl: null })} + > + { + availablePlots.map(availablePlot => ( + this.setState({ selectedPlot: availablePlot })} + > + {availablePlot.name} + + )) + } + + + this.clickAddToWidget(color)} + /> + + + + } -} \ No newline at end of file +} diff --git a/webapp/components/reduxconnect/AddPlotMenuConnect.js b/webapp/components/reduxconnect/AddPlotMenuConnect.js index dc18ac0..2e3d9bf 100644 --- a/webapp/components/reduxconnect/AddPlotMenuConnect.js +++ b/webapp/components/reduxconnect/AddPlotMenuConnect.js @@ -3,7 +3,7 @@ import AddPlotMenu from '../AddPlotMenu'; const mapStateToProps = (state, ownProps) => ({ icon: ownProps.icon, - widgets: state.flexlayout.widgets + widgets: Object.values(state.flexlayout.widgets).filter(w => w.component == "Plot").map(w => ({ instancePath: w.instancePath, id: w.id, name: w.name, guestList: w.guestList })) }); -export default connect(mapStateToProps)(AddPlotMenu) \ No newline at end of file +export default connect(mapStateToProps)(AddPlotMenu); \ No newline at end of file diff --git a/webapp/middleware/nwbMiddleware.js b/webapp/middleware/nwbMiddleware.js index 9e99b70..4338518 100644 --- a/webapp/middleware/nwbMiddleware.js +++ b/webapp/middleware/nwbMiddleware.js @@ -75,7 +75,7 @@ function handlePlotTimeseries (store, next, action) { } const nwbMiddleware = store => next => action => { - + console.log(action); switch (action.type) { case LOAD_NWB_FILE: From 835cadd528b6003db9955600e4b9f357a26eeb86 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 8 Apr 2020 14:46:37 +0200 Subject: [PATCH 30/42] #129 Fixe interface bugs on firefox --- webapp/components/LayoutManager.js | 20 +++++++++----------- webapp/styles/main.less | 19 ++++++++++++++----- 2 files changed, 23 insertions(+), 16 deletions(-) diff --git a/webapp/components/LayoutManager.js b/webapp/components/LayoutManager.js index 74b5b22..2ec5b97 100644 --- a/webapp/components/LayoutManager.js +++ b/webapp/components/LayoutManager.js @@ -281,20 +281,18 @@ export default class LayoutManager extends Component { } } } + render () { return ( -
- this.onAction(action)} - clickOnBordersAction={node => this.clickOnBordersAction(node)} - onRenderTabSet={(node, renderValues) => this.onRenderTabSet(node, renderValues)} - /> - -
+ this.onAction(action)} + clickOnBordersAction={node => this.clickOnBordersAction(node)} + onRenderTabSet={(node, renderValues) => this.onRenderTabSet(node, renderValues)} + /> ) } } \ No newline at end of file diff --git a/webapp/styles/main.less b/webapp/styles/main.less index 54af3f4..d9bdaa6 100644 --- a/webapp/styles/main.less +++ b/webapp/styles/main.less @@ -108,9 +108,12 @@ iframe{ margin-bottom: 0; } .flexlayout__layout { - - margin-top:20px; - margin-bottom:40px; + position: relative; + top: 0; + bottom: 0; + margin-bottom: 40px; + + flex: 1; a { color: @color-link; } @@ -293,7 +296,12 @@ iframe{ } #mainContainer, #mainContainer > div, #main-container-inner { height: 100%; - + display: flex; + flex-direction: column; + .MuiGrid-item { + padding-top: 0; + padding-bottom: 0; + } } .center-filler { @@ -594,4 +602,5 @@ iframe{ .gpt-addplot:before { vertical-align: -5px; font-size: 23px; -} \ No newline at end of file +} + From ed6fb1442b461ee174136905cc805e14dd8d5d92 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 8 Apr 2020 14:46:56 +0200 Subject: [PATCH 31/42] Remove actions logging --- webapp/middleware/nwbMiddleware.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/webapp/middleware/nwbMiddleware.js b/webapp/middleware/nwbMiddleware.js index 4338518..cbd8c5e 100644 --- a/webapp/middleware/nwbMiddleware.js +++ b/webapp/middleware/nwbMiddleware.js @@ -75,7 +75,7 @@ function handlePlotTimeseries (store, next, action) { } const nwbMiddleware = store => next => action => { - console.log(action); + // console.log(action); switch (action.type) { case LOAD_NWB_FILE: From 51dae5d3d9da313e9487243514e5b39556502269 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Thu, 9 Apr 2020 10:24:06 +0200 Subject: [PATCH 32/42] Small refactor on cookie loading --- webapp/components/App.js | 11 +---------- webapp/services/NWBFileService.js | 10 ++++++++++ 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/webapp/components/App.js b/webapp/components/App.js index 8f29755..bcba6e2 100644 --- a/webapp/components/App.js +++ b/webapp/components/App.js @@ -35,16 +35,7 @@ export default class App extends React.Component{ componentDidMount () { const { loadNWBFile, loadNotebook, notebookReady, nwbFileLoaded, raiseError } = this.props; self = this; - - const cookieName = 'nwbloadurl'; - const nwbCookie = document.cookie.split(';').find(cookie => cookie.includes(cookieName)) - if (nwbCookie) { - const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("="); - if (nwbFileUrl) { - document.cookie = `${cookieName}= ; path=/`; - loadNWBFile(nwbFileUrl); - } - } + GEPPETTO.on(GEPPETTO.Events.Error_while_exec_python_command, error => { if (error) { diff --git a/webapp/services/NWBFileService.js b/webapp/services/NWBFileService.js index 10df2d6..798bab6 100644 --- a/webapp/services/NWBFileService.js +++ b/webapp/services/NWBFileService.js @@ -15,6 +15,16 @@ class NWBFileService { if (urlParams.get(NWB_FILE_URL_PARAM)) { return urlParams.get(NWB_FILE_URL_PARAM); } + + const cookieName = 'nwbloadurl'; + const nwbCookie = document.cookie.split(';').find(cookie => cookie.includes(cookieName)) + if (nwbCookie) { + const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("="); + if (nwbFileUrl) { + document.cookie = `${cookieName}= ; path=/`; + return nwbFileUrl; + } + } return null; } From 251aba732971860a9a2a3055b5a924a4e7f8cf0f Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Thu, 9 Apr 2020 15:28:36 +0200 Subject: [PATCH 33/42] Release 0.4.0 version update --- setup.py | 2 +- webapp/package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/setup.py b/setup.py index 81ff07b..fbb9427 100644 --- a/setup.py +++ b/setup.py @@ -16,7 +16,7 @@ setuptools.setup( name="nwb_explorer", - version="0.3", + version="0.4", url="https://github.com/tarelli/nwb-explorer", author="MetaCell", author_email="info@metacell.us", diff --git a/webapp/package.json b/webapp/package.json index 3aee6dc..ae85adc 100644 --- a/webapp/package.json +++ b/webapp/package.json @@ -1,6 +1,6 @@ { "name": "nwb-explorer", - "version": "0.3.0", + "version": "0.4.0", "description": "NWB Explorer is an application that can be used by scientists to read, visualize and explore the content of NWB 2 files.", "repository": "https://github.com/MetaCell/geppetto-nwbexplorer", "license": "MIT", From 992fb4108d734fa9fce04769da2503fb4df92ca9 Mon Sep 17 00:00:00 2001 From: jrmartin Date: Mon, 13 Apr 2020 16:48:41 -0700 Subject: [PATCH 34/42] Adds experimenter to metadata summary --- nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index bbe4bc5..0f06f33 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -346,12 +346,14 @@ def build_fields(self, nwbfile): ''' Use this function to add the fields you want to see in the Geppetto model ''' aqc = len(nwbfile.acquisition) stim = len(nwbfile.stimulus) + experimenter = len(nwbfile.experimenter) summary = {} if aqc: summary['Num. of acquisitions'] = f"{aqc}" if stim: summary['Num. of stimuli'] = f"{stim}" - + if experimenter: + summary['experimenter'] = f"{nwbfile.experimenter[0]}" return summary def modify_type(self, pynwb_obj, geppetto_composite_type): From 79f990d7858199b303439a2e0c2035300da9e4fc Mon Sep 17 00:00:00 2001 From: jrmartin Date: Tue, 14 Apr 2020 08:37:28 -0700 Subject: [PATCH 35/42] join array of strings for experimenter, might be more than one experimenter in the list --- nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 0f06f33..ac8b3d2 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -353,7 +353,7 @@ def build_fields(self, nwbfile): if stim: summary['Num. of stimuli'] = f"{stim}" if experimenter: - summary['experimenter'] = f"{nwbfile.experimenter[0]}" + summary['experimenter'] = f"{','.join(nwbfile.experimenter)}" return summary def modify_type(self, pynwb_obj, geppetto_composite_type): From a59240dd01d5b1d9539a6df58439d26b56450866 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Tue, 5 May 2020 20:47:59 +0200 Subject: [PATCH 36/42] #157 fixing jupyterhub get uri and redirect --- k8s/auth.py | 2 +- webapp/package.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/k8s/auth.py b/k8s/auth.py index d337354..4a82bc2 100644 --- a/k8s/auth.py +++ b/k8s/auth.py @@ -36,7 +36,7 @@ def get(self): redirection = self.get_next_url(user) user.spawners[server_name].environment["NWBFILE"] = '' - if 'hub/nwbfile=' in self.request.uri: + if 'nwbfile=' in self.request.uri: server_name = str(uuid.uuid4()).split('-').pop() redirection = f'/hub/spawn/{user.name}/{server_name}' url = self.request.uri.split('=').pop() diff --git a/webapp/package.json b/webapp/package.json index ae85adc..7cbfc5e 100644 --- a/webapp/package.json +++ b/webapp/package.json @@ -6,7 +6,7 @@ "license": "MIT", "scripts": { "prebuild": "eslint . --color", - "build": "webpack --mode production -p --progress", + "build": "webpack --mode production -p --devtool source-map", "prebuild-dev": "eslint . --color", "build-dev": "webpack --mode development --devtool eval", "prebuild-dev-noTest": "eslint . ", From 095a728f8273b0e9dba42cba704d966d7e654569 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 10:07:24 +0200 Subject: [PATCH 37/42] #157 Loading from cookie fixed --- webapp/services/NWBFileService.js | 25 ++++++++++++++----------- 1 file changed, 14 insertions(+), 11 deletions(-) diff --git a/webapp/services/NWBFileService.js b/webapp/services/NWBFileService.js index 798bab6..15c7874 100644 --- a/webapp/services/NWBFileService.js +++ b/webapp/services/NWBFileService.js @@ -11,21 +11,24 @@ class NWBFileService { } getNWBFileUrl () { + let urlParams = new URLSearchParams(window.location.search); if (urlParams.get(NWB_FILE_URL_PARAM)) { - return urlParams.get(NWB_FILE_URL_PARAM); - } - - const cookieName = 'nwbloadurl'; - const nwbCookie = document.cookie.split(';').find(cookie => cookie.includes(cookieName)) - if (nwbCookie) { - const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("="); - if (nwbFileUrl) { - document.cookie = `${cookieName}= ; path=/`; - return nwbFileUrl; + this.nwbfile = urlParams.get(NWB_FILE_URL_PARAM); + } else { + const cookieName = 'nwbloadurl'; + const nwbCookie = document.cookie.split(';').find(cookie => cookie.includes(cookieName)) + if (nwbCookie) { + const [_, nwbFileUrl] = nwbCookie.replace(/"/g, '').split("="); + if (nwbFileUrl) { + document.cookie = `${cookieName}= ; path=/`; + this.nwbfile = nwbFileUrl; + } } } - return null; + + + return this.nwbfile; } From 7cea952483020db34fae525eed1a579750539b45 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 10:30:58 +0200 Subject: [PATCH 38/42] #159 enabled jupyter widgets #144 upgrade pynwb --- nwb_explorer/api.py | 1 + nwb_explorer/nwb_main.py | 9 ++++++--- requirements.txt | 4 ++-- setup.py | 2 +- utilities/custom.css | 10 ++++++++++ 5 files changed, 20 insertions(+), 6 deletions(-) diff --git a/nwb_explorer/api.py b/nwb_explorer/api.py index 65ffd7b..52186db 100644 --- a/nwb_explorer/api.py +++ b/nwb_explorer/api.py @@ -29,6 +29,7 @@ def createNotebook(filename): With this Python console you can programmatically access the loaded data using the [PyNWB Python API](https://pynwb.readthedocs.io/en/stable/). The loaded NWB:N 2 file can be accessed from the variable `nwbfile`. +If you would like to inspect the content of the file using the [NWB Juypyter widgets](https://pypi.org/project/nwbwidgets/) you can use the `show()` function. To execute a command type it and press `Shift+Enter`. To execute a command and create a new cell press `Alt+Enter`."""), nbf.v4.new_code_cell('nwbfile') diff --git a/nwb_explorer/nwb_main.py b/nwb_explorer/nwb_main.py index 91eb683..45d79d4 100644 --- a/nwb_explorer/nwb_main.py +++ b/nwb_explorer/nwb_main.py @@ -47,8 +47,11 @@ def main(nwbfilename): # pytest: no cover main = __import__('__main__') - from nwbwidgets import nwb2widget - main.nwb2widget = nwb2widget - main.show = lambda: nwb2widget(main.nwbfile) + + def show(): + from nwbwidgets import nwb2widget + main.nwb2widget = nwb2widget + nwb2widget(main.nwbfile) + main.show = show logging.info("NWB UI initialised") \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 79f68e2..f093bc4 100644 --- a/requirements.txt +++ b/requirements.txt @@ -55,7 +55,7 @@ ndx-grayscalevolume==0.0.2 nose==1.3.7 notebook==5.6.0 numpy==1.18.1 -nwbwidgets==0.0.2 +nwbwidgets==0.2.0 ordered-set==3.0.1 packaging==19.1 pandas==0.25.3 @@ -77,7 +77,7 @@ pyecore==0.10.2 pygeppetto==0.6.0 Pygments==2.2.0 pymultigen==0.2.0 -pynwb==1.2.1 +pynwb==1.3.0 pyparsing==2.2.0 pyrsistent==0.15.4 python-dateutil==2.8.0 diff --git a/setup.py b/setup.py index fbb9427..820efd4 100644 --- a/setup.py +++ b/setup.py @@ -53,6 +53,6 @@ 'imageio>=2.5.0', 'quantities>=0.12.3', 'hdmf==1.5.4', - 'nwbwidgets>=0.0.2' + 'nwbwidgets>=0.2.0' ], ) diff --git a/utilities/custom.css b/utilities/custom.css index a6990e6..a5f8f0c 100644 --- a/utilities/custom.css +++ b/utilities/custom.css @@ -13,4 +13,14 @@ .text_cell_render code { color: #EDB53D; background: transparent; +} + +.jupyter-widgets-view .p-Widget, .jupyter-widgets-view .widget-label{ + background-color: transparent !important; + color: white !important; +} + + +.jupyter-widgets-view .output_png { + background-color: #aaa !important; } \ No newline at end of file From 4832d5dee14e326c5367444b6d2a7b8c2ae4d967 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 11:20:42 +0200 Subject: [PATCH 39/42] #157 Fix show command --- nwb_explorer/nwb_main.py | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/nwb_explorer/nwb_main.py b/nwb_explorer/nwb_main.py index 45d79d4..91eb683 100644 --- a/nwb_explorer/nwb_main.py +++ b/nwb_explorer/nwb_main.py @@ -47,11 +47,8 @@ def main(nwbfilename): # pytest: no cover main = __import__('__main__') - - def show(): - from nwbwidgets import nwb2widget - main.nwb2widget = nwb2widget - nwb2widget(main.nwbfile) - main.show = show + from nwbwidgets import nwb2widget + main.nwb2widget = nwb2widget + main.show = lambda: nwb2widget(main.nwbfile) logging.info("NWB UI initialised") \ No newline at end of file From 1ba8d0324d09d39e4e12596131d677952ea7d951 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 15:09:37 +0200 Subject: [PATCH 40/42] Improved list metadata --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index ac8b3d2..5243057 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -83,6 +83,12 @@ def creates(self, value): def create_variable(self, name, pynwb_obj, parent_obj): return self.model_factory.create_text_variable(id=name, text=str(pynwb_obj)) +class ListMapper(NWBGeppettoMapper): + def creates(self, value): + return is_collection(value) and value and is_metadata(next(iter(value))) + + def create_variable(self, name, pynwb_obj, parent_obj): + return self.model_factory.create_text_variable(id=name, text=str(','.join(str(o) for o in pynwb_obj))) class ImportValueMapper(NWBGeppettoMapper): @@ -346,14 +352,12 @@ def build_fields(self, nwbfile): ''' Use this function to add the fields you want to see in the Geppetto model ''' aqc = len(nwbfile.acquisition) stim = len(nwbfile.stimulus) - experimenter = len(nwbfile.experimenter) summary = {} if aqc: summary['Num. of acquisitions'] = f"{aqc}" if stim: summary['Num. of stimuli'] = f"{stim}" - if experimenter: - summary['experimenter'] = f"{','.join(nwbfile.experimenter)}" + return summary def modify_type(self, pynwb_obj, geppetto_composite_type): From 48e7ef5c7dd0b0a9c6d652faa5f700a1c567c9e0 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 15:36:23 +0200 Subject: [PATCH 41/42] Generalized array object display --- .../nwb_model_interpreter/nwb_geppetto_mappers.py | 10 +++++----- webapp/components/Metadata.js | 5 +++++ 2 files changed, 10 insertions(+), 5 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 5243057..39bee7d 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -83,12 +83,12 @@ def creates(self, value): def create_variable(self, name, pynwb_obj, parent_obj): return self.model_factory.create_text_variable(id=name, text=str(pynwb_obj)) -class ListMapper(NWBGeppettoMapper): - def creates(self, value): - return is_collection(value) and value and is_metadata(next(iter(value))) +# class ListMapper(NWBGeppettoMapper): +# def creates(self, value): +# return is_collection(value) and value and is_metadata(next(iter(value))) - def create_variable(self, name, pynwb_obj, parent_obj): - return self.model_factory.create_text_variable(id=name, text=str(','.join(str(o) for o in pynwb_obj))) +# def create_variable(self, name, pynwb_obj, parent_obj): +# return self.model_factory.create_text_variable(id=name, text=str(','.join(str(o) for o in pynwb_obj))) class ImportValueMapper(NWBGeppettoMapper): diff --git a/webapp/components/Metadata.js b/webapp/components/Metadata.js index 898456d..33de5c1 100644 --- a/webapp/components/Metadata.js +++ b/webapp/components/Metadata.js @@ -65,6 +65,11 @@ export default class Metadata extends React.Component { } else if (variableType.getChildren && variableType.getChildren()) { metadata = variable.getType().getChildren().filter(v => v.getType().getName() == 'Text').map(v => this.formatField(prettyLabel(v.getId()), this.prettyContent(v.getInitialValue().value.text))); + } else if (variableType.getName() == 'Simple Array') { + metadata = variable.getInitialValue().value.elements.join(','); + console.log('Array:', metadata); + } else { + console.debug('Unsupported variable', variable) } if (metadata && (metadata.length || metadata.type)) { From 3e09800d9c40dc8120a06ec2b3f5c9207b95ae65 Mon Sep 17 00:00:00 2001 From: Filippo Ledda Date: Wed, 6 May 2020 15:37:17 +0200 Subject: [PATCH 42/42] chore clean useless code --- .../nwb_geppetto_mappers.py | 7 --- webapp/webpack.config.dev.js | 61 +++++++++++++++---- 2 files changed, 48 insertions(+), 20 deletions(-) diff --git a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py index 39bee7d..2aa3f54 100644 --- a/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py +++ b/nwb_explorer/nwb_model_interpreter/nwb_geppetto_mappers.py @@ -83,13 +83,6 @@ def creates(self, value): def create_variable(self, name, pynwb_obj, parent_obj): return self.model_factory.create_text_variable(id=name, text=str(pynwb_obj)) -# class ListMapper(NWBGeppettoMapper): -# def creates(self, value): -# return is_collection(value) and value and is_metadata(next(iter(value))) - -# def create_variable(self, name, pynwb_obj, parent_obj): -# return self.model_factory.create_text_variable(id=name, text=str(','.join(str(o) for o in pynwb_obj))) - class ImportValueMapper(NWBGeppettoMapper): def creates(self, value): diff --git a/webapp/webpack.config.dev.js b/webapp/webpack.config.dev.js index cb3c7c8..1fa68b6 100644 --- a/webapp/webpack.config.dev.js +++ b/webapp/webpack.config.dev.js @@ -1,23 +1,58 @@ var webpackBaseConfig = require('./webpack.config.js'); var extended = webpackBaseConfig(); + extended.devServer = { - progress : true, + progress : false, port : 8081, inline : true, + publicPath: '/geppetto/build', + + proxy : [ + { + path : '/', + target : 'http://localhost:8888' + }, + { + path : '/org.geppetto.frontend', + target : 'ws://localhost:8888', + ws : true + }, + { + path : '/notebooks', + target : 'http://localhost:8888' + }, + { + path : '/api', + target : 'http://localhost:8888' + }, + { + path : '/api/kernels', + target : 'ws://localhost:8888', + ws: true + }, + { + path : '/static', + target : 'http://localhost:8888' + }, + { + path : '/custom', + target : 'http://localhost:8888' + }, + + { + path : '/nbextensions', + target : 'http://localhost:8888' + }, + ], +}; + - proxy : [ { - path : '/', - target : 'http://localhost:8080/' - }, { - path : '/geppetto', - target : 'http://localhost:8080/org.geppetto.frontend' - }, { - path : '/org.geppetto.frontend', - target : 'ws://localhost:8080', - ws : true - }, ], +extended.optimization = { + ...extended.optimization, + removeAvailableModules: false, + removeEmptyChunks: false, }; extended.devtool = 'source-map'; -module.exports = extended; +module.exports = extended; \ No newline at end of file