Merge pull request #6 from databricks-industry-solutions/fix/linkfeedback

Update README.md - fix relative link to notebook

Author: dmoore247

README.md

@@ -25,6 +25,7 @@ Please see our [installation guide](./INSTALL.md)
 
 © 2025 Databricks, Inc. All rights reserved. The source in this project is provided subject to the Databricks License [https://databricks.com/db-license-source]. All included or referenced third party libraries are subject to the licenses set forth below.
 
-| Package | Purpose | License | Source |
-|---------|---------|---------|--------|
-| pydicom	| Python api for DICOM files |	MIT	| https://github.com/pydicom/pydicom |
+| Datasource | Package    | Purpose                           | License     | Source                               |
+| ---------- | ---------- | --------------------------------- | ----------- | ------------------------------------ |
+| zipdcm     | pydicom	  | Python api for DICOM files        |	MIT	        | https://github.com/pydicom/pydicom   |
+| zipdcm     | pylibjpeg  | Decoding / Encoding pixel formats | GPLv3 & MIT | https://github.com/pydicom/pylibjpeg |

zipdcm/README.md

@@ -8,10 +8,15 @@ from dbx.zip_dcm_ds import ZipDCMDataSource
 spark.dataSource.register(ZipDCMDataSource)
 
 # read DCMs with `numPartitions` parallelism.
-df = spark.read.format("zipdcm").option('numPartitions',4).load("./resources")
+df = (
+    spark.read
+    .format("zipdcm")
+    .option("numPartitions",4)
+    .load("./resources")
+)
 df.display()
 ```
-For more, see our [demo]($./demo) notebook.
+For more, see our [demo](./zip-dicom-demo.ipynb) notebook.
 
 ## Install
 
@@ -38,3 +43,6 @@ Run unit tests
 ```bash
 make test
 ```
+
+### Synthetic PHI data source citation
+Rutherford, M. W., Nolan, T., Pei, L., Wagner, U., Pan, Q., Farmer, P., Smith, K., Kopchick, B., Laura Opsahl-Ong, Sutton, G., Clunie, D. A., Farahani, K., & Prior, F. (2025). Data in Support of the MIDI-B Challenge (MIDI-B-Synthetic-Validation, MIDI-B-Curated-Validation, MIDI-B-Synthetic-Test, MIDI-B-Curated-Test) (Version 1) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/CF2P-AW56 

zipdcm/requirements.txt

@@ -1,2 +1,3 @@
 pydicom==3.0.1
+pylibjpeg[all]>=2.0.1
 pyspark==4.0.0.dev1

zipdcm/zip-dicom-demo.ipynb

@@ -19,11 +19,14 @@
     "# Read Zipped DICOM files saving time and storage\n",
     "WIth the custom \"zipdcm\" Python Data Source, we can read zipped (and non Zipped) up DICOM files directly to extract their metadata.\n",
     "\n",
-    "Requirements:\n",
-    "- Recommend DBR 17.0 (Apache Spark 4.0) compute\n",
+    "### Requirements:\n",
+    "- Recommend DBR 17.1 (Apache Spark 4.0) dedicated compute\n",
     "- Shared cluster compute compatible\n",
     "- Working on serverless compute fix.\n",
-    "- Requires `pydicom==3.0.1`"
+    "- Requires `pydicom==3.0.1 pylibjpeg[all]>=2.0.1`\n",
+    "\n",
+    "### Synthetic PHI data source citation\n",
+    "Rutherford, M. W., Nolan, T., Pei, L., Wagner, U., Pan, Q., Farmer, P., Smith, K., Kopchick, B., Laura Opsahl-Ong, Sutton, G., Clunie, D. A., Farahani, K., & Prior, F. (2025). Data in Support of the MIDI-B Challenge (MIDI-B-Synthetic-Validation, MIDI-B-Curated-Validation, MIDI-B-Synthetic-Test, MIDI-B-Curated-Test) (Version 1) [Dataset]. The Cancer Imaging Archive. https://doi.org/10.7937/CF2P-AW56 "
    ]
   },
   {
@@ -53,7 +56,8 @@
     }
    ],
    "source": [
-    "%pip install --quiet pydicom==3.0.1\n",
+    "# %pip install --quiet numpy==1.26.4 pydicom==3.0.1 pylibjpeg[all]>=2.0.1\n",
+    "%pip install --quiet numpy==2.1.3  pydicom==3.0.1 pylibjpeg[all]>=2.0.1\n",
     "%restart_python"
    ]
   },
@@ -79,7 +83,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "total 57M\n-rwxrwxrwx 1 root root  12K Aug  1 21:09 1.3.199.1.2.3712432.1.402.1107814368275696879.zip\n-rwxrwxrwx 1 root root  24M Aug  1 21:09 3.5.574.1.3.9030958.6.376.1780887819048872979.zip\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 3.5.574.1.3.9030958.6.376.2860280475000825621.zip\ndrwxrwxrwx 2 root root 4.0K Aug  2 17:33 x\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 x.zip\ndrwxrwxrwx 2 root root 4.0K Aug  2 17:33 y\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 y.zip\n"
+      "total 57M\n-rwxrwxrwx 1 root root  12K Aug  1 21:09 1.3.199.1.2.3712432.1.402.1107814368275696879.zip\n-rwxrwxrwx 1 root root  24M Aug  1 21:09 3.5.574.1.3.9030958.6.376.1780887819048872979.zip\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 3.5.574.1.3.9030958.6.376.2860280475000825621.zip\ndrwxrwxrwx 2 root root 4.0K Aug 10 04:17 x\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 x.zip\ndrwxrwxrwx 2 root root 4.0K Aug 10 04:17 y\n-rwxrwxrwx 1 root root  12M Aug  1 21:09 y.zip\n"
      ]
     }
    ],
@@ -213,24 +217,35 @@
     "spark.dataSource.register(ZipDCMDataSource)\n",
     "\n",
     "# read DCMs with `numPartitions` parallelism.\n",
-    "df = spark.read.format(\"zipdcm\").option('numPartitions',4).load(\"./resources\")\n",
+    "df = (\n",
+    "    spark.read\n",
+    "    .format(\"zipdcm\")\n",
+    "    .option(\"numPartitions\",4)\n",
+    "    .load(\"./resources\")\n",
+    ")\n",
     "df.display()"
    ]
   }
  ],
  "metadata": {
   "application/vnd.databricks.v1+notebook": {
-   "computePreferences": null,
+   "computePreferences": {
+    "hardware": {
+     "accelerator": null,
+     "gpuPoolId": null,
+     "memory": null
+    }
+   },
    "dashboards": [],
    "environmentMetadata": {
-    "base_environment": "dbe_65bc13ea-276c-4905-a728-9fe2fb1780e2",
+    "base_environment": "",
     "environment_version": "2"
    },
    "inputWidgetPreferences": null,
    "language": "python",
    "notebookMetadata": {
     "mostRecentlyExecutedCommandWithImplicitDF": {
-     "commandId": 7424973428825328,
+     "commandId": 5816783787054213,
      "dataframes": [
       "_sqldf"
      ]