update examples

.idea/.gitignore

@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml

.idea/inspectionProfiles/Project_Default.xml

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+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ignoredPackages">
+        <value>
+          <list size="64">
+            <item index="0" class="java.lang.String" itemvalue="pandas" />
+            <item index="1" class="java.lang.String" itemvalue="kaleido" />
+            <item index="2" class="java.lang.String" itemvalue="plotly" />
+            <item index="3" class="java.lang.String" itemvalue="numpy" />
+            <item index="4" class="java.lang.String" itemvalue="tensorflow_probability" />
+            <item index="5" class="java.lang.String" itemvalue="tensorflow_addons" />
+            <item index="6" class="java.lang.String" itemvalue="Jinja2" />
+            <item index="7" class="java.lang.String" itemvalue="scipy" />
+            <item index="8" class="java.lang.String" itemvalue="statsmodels" />
+            <item index="9" class="java.lang.String" itemvalue="pytz" />
+            <item index="10" class="java.lang.String" itemvalue="dash_core_components" />
+            <item index="11" class="java.lang.String" itemvalue="Werkzeug" />
+            <item index="12" class="java.lang.String" itemvalue="dash_html_components" />
+            <item index="13" class="java.lang.String" itemvalue="MarkupSafe" />
+            <item index="14" class="java.lang.String" itemvalue="dash" />
+            <item index="15" class="java.lang.String" itemvalue="flask" />
+            <item index="16" class="java.lang.String" itemvalue="itsdangerous" />
+            <item index="17" class="java.lang.String" itemvalue="click" />
+            <item index="18" class="java.lang.String" itemvalue="dash_renderer" />
+            <item index="19" class="java.lang.String" itemvalue="gunicorn" />
+            <item index="20" class="java.lang.String" itemvalue="tensorflow" />
+            <item index="21" class="java.lang.String" itemvalue="torch" />
+            <item index="22" class="java.lang.String" itemvalue="gensim" />
+            <item index="23" class="java.lang.String" itemvalue="torchtext" />
+            <item index="24" class="java.lang.String" itemvalue="nltk" />
+            <item index="25" class="java.lang.String" itemvalue="h5py" />
+            <item index="26" class="java.lang.String" itemvalue="progressbar2" />
+            <item index="27" class="java.lang.String" itemvalue="torchvision" />
+            <item index="28" class="java.lang.String" itemvalue="Pillow" />
+            <item index="29" class="java.lang.String" itemvalue="dash-renderer" />
+            <item index="30" class="java.lang.String" itemvalue="dash_table" />
+            <item index="31" class="java.lang.String" itemvalue="scikit-learn" />
+            <item index="32" class="java.lang.String" itemvalue="absl-py" />
+            <item index="33" class="java.lang.String" itemvalue="protobuf" />
+            <item index="34" class="java.lang.String" itemvalue="rsa" />
+            <item index="35" class="java.lang.String" itemvalue="tensorflow-estimator" />
+            <item index="36" class="java.lang.String" itemvalue="pycodestyle" />
+            <item index="37" class="java.lang.String" itemvalue="requests" />
+            <item index="38" class="java.lang.String" itemvalue="requests-oauthlib" />
+            <item index="39" class="java.lang.String" itemvalue="certifi" />
+            <item index="40" class="java.lang.String" itemvalue="oauthlib" />
+            <item index="41" class="java.lang.String" itemvalue="keras" />
+            <item index="42" class="java.lang.String" itemvalue="tomli" />
+            <item index="43" class="java.lang.String" itemvalue="urllib3" />
+            <item index="44" class="java.lang.String" itemvalue="pyparsing" />
+            <item index="45" class="java.lang.String" itemvalue="Markdown" />
+            <item index="46" class="java.lang.String" itemvalue="autopep8" />
+            <item index="47" class="java.lang.String" itemvalue="libclang" />
+            <item index="48" class="java.lang.String" itemvalue="tensorboard-data-server" />
+            <item index="49" class="java.lang.String" itemvalue="wrapt" />
+            <item index="50" class="java.lang.String" itemvalue="kiwisolver" />
+            <item index="51" class="java.lang.String" itemvalue="packaging" />
+            <item index="52" class="java.lang.String" itemvalue="tensorflow-io-gcs-filesystem" />
+            <item index="53" class="java.lang.String" itemvalue="fonttools" />
+            <item index="54" class="java.lang.String" itemvalue="termcolor" />
+            <item index="55" class="java.lang.String" itemvalue="flatbuffers" />
+            <item index="56" class="java.lang.String" itemvalue="tensorboard" />
+            <item index="57" class="java.lang.String" itemvalue="typing_extensions" />
+            <item index="58" class="java.lang.String" itemvalue="cachetools" />
+            <item index="59" class="java.lang.String" itemvalue="charset-normalizer" />
+            <item index="60" class="java.lang.String" itemvalue="grpcio" />
+            <item index="61" class="java.lang.String" itemvalue="google-auth" />
+            <item index="62" class="java.lang.String" itemvalue="idna" />
+            <item index="63" class="java.lang.String" itemvalue="matplotlib" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="E101" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyTypeCheckerInspection" enabled="false" level="WARNING" enabled_by_default="false" />
+  </profile>
+</component>

.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

.idea/misc.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8" project-jdk-type="Python SDK" />
+  <component name="PyPackaging">
+    <option name="earlyReleasesAsUpgrades" value="true" />
+  </component>
+</project>

.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/pubmed-clip-vit-base-patch32.iml" filepath="$PROJECT_DIR$/.idea/pubmed-clip-vit-base-patch32.iml" />
+    </modules>
+  </component>
+</project>

.idea/pubmed-clip-vit-base-patch32.iml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="inheritedJdk" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="PLAIN" />
+    <option name="myDocStringFormat" value="Plain" />
+  </component>
+</module>

.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="" vcs="Git" />
+  </component>
+</project>

scripts/flax_example.py

@@ -0,0 +1,23 @@
+import jax
+import requests
+from PIL import Image
+import matplotlib.pyplot as plt
+
+from transformers import CLIPProcessor, FlaxCLIPModel
+
+model = FlaxCLIPModel.from_pretrained("flaviagiammarino/pubmed-clip-vit-base-patch32")
+processor = CLIPProcessor.from_pretrained("flaviagiammarino/pubmed-clip-vit-base-patch32")
+
+url = "https://d168r5mdg5gtkq.cloudfront.net/medpix/img/full/synpic9078.jpg"
+image = Image.open(requests.get(url, stream=True).raw)
+text = ["Chest X-Ray", "Brain MRI", "Abdominal CT Scan"]
+
+inputs = processor(text=text, images=image, return_tensors="jax", padding=True)
+probs = jax.nn.softmax(model(**inputs).logits_per_image, axis=-1).flatten()
+
+plt.subplots()
+plt.imshow(image)
+plt.title("".join([x[0] + ": " + x[1] + "\n" for x in zip(text, [format(prob, ".4%") for prob in probs])]))
+plt.axis("off")
+plt.tight_layout()
+plt.show()

scripts/pt_example.py

@@ -12,7 +12,7 @@ image = Image.open(requests.get(url, stream=True).raw)
 text = ["Chest X-Ray", "Brain MRI", "Abdominal CT Scan"]
 
 inputs = processor(text=text, images=image, return_tensors="pt", padding=True)
-probs = model(**inputs).logits_per_image.softmax(dim=1).detach().numpy().flatten()
+probs = model(**inputs).logits_per_image.softmax(dim=1).squeeze()
 
 plt.subplots()
 plt.imshow(image)

scripts/tf_example.py

@@ -13,7 +13,7 @@ image = Image.open(requests.get(url, stream=True).raw)
 text = ["Chest X-Ray", "Brain MRI", "Abdominal CT Scan"]
 
 inputs = processor(text=text, images=image, return_tensors="tf", padding=True)
-probs = tf.nn.softmax(model(**inputs).logits_per_image, axis=-1).numpy().flatten()
+probs = tf.squeeze(tf.nn.softmax(model(**inputs).logits_per_image, axis=-1))
 
 plt.subplots()
 plt.imshow(image)