FFMPEG command to crop and transpose video comes out zoomed in bad quality

Question

I'm trying to convert an mp4 video with dimensions usually 960x720 into a sqaure 480:480 video but it comes out looking squished usually, the command is

"-y -i %s -vf crop=480:480,transpose=%d -threads 5 -metadata:s:v rotate=0 -c:v libx264 -crf 27 -preset ultrafast -c:a copy -bsf:a aac_adtstoasc %s";

Am I missing something, do I need to down scale first or something?

**EDIT adding full console output. The ffmpeg command is updated, but the goal still remains the same, take an arbitrary video and square crop it

07-14 22:30:32.813: D/ffmpeg(30354): -y -i /data/data/com.myapp.app/cache:temp/i7h4ajm0nim1mbcnrqotvrhhsc.mp4 -vf scale=iw*sar:ih,transpose=1 -threads 5 -metadata:s:v rotate=0 -c:v libx264 -crf 27 -preset ultrafast -c:a copy -bsf:a aac_adtstoasc -aspect 1:1 /data/data/com.myapp.app/cache:temp/p1t3bhs0oa3lpqa67g5i9ninm9.ts
07-14 22:30:32.903: D/ffmpeg(30354): new time reamining 9283
07-14 22:30:32.913: D/FFmpeg(30354): Running publishing updates method
07-14 22:30:35.963: D/ffmpeg(30354): WARNING: linker: /data/data/com.myapp.app/files/ffmpeg has text relocations. This is wasting memory and prevents security hardening. Please fix.
07-14 22:30:35.963: D/ffmpeg(30354): ffmpeg version n2.4.2 Copyright (c) 2000-2014 the FFmpeg developers
07-14 22:30:35.963: D/ffmpeg(30354):   built on Jun  3 2015 21:56:01 with gcc 4.8 (GCC)
07-14 22:30:35.963: D/ffmpeg(30354):   configuration: --target-os=linux --cross-prefix=/Users/Brian1/development/ffmpeg-android/toolchain-android/bin/arm-linux-androideabi- --arch=arm --cpu=cortex-a8 --enable-runtime-cpudetect --sysroot=/Users/Brian1/development/ffmpeg-android/toolchain-android/sysroot --enable-pic --enable-small --enable-libx264 --enable-pthreads --disable-muxers --enable-muxer=mpegts --enable-muxer=mp4 --disable-demuxers --enable-demuxer=mpegts --enable-demuxer=mov --enable-demuxer=mpeg --enable-demuxer=mp4 --disable-debug --disable-decoders --enable-decoder=h264 --enable-decoder=aac --disable-devices --disable-encoders --enable-encoder=libx264 --disable-network --disable-ffserver --enable-version3 --enable-hardcoded-tables --disable-ffplay --disable-ffprobe --enable-gpl --enable-yasm --disable-doc --disable-shared --enable-static --pkg-config=/Users/Brian1/development/ffmpeg-android/ffmpeg-pkg-config --prefix=/Users/Brian1/development/ffmpeg-android/build/armeabi-v7a-neon --extra-cflags='-I/Users/Brian1/development/ffmpeg-android/toolchain-android/include -U_FORTIFY_SOURCE -D_FORTIFY_SOURCE=2 -fno-strict-overflow -fstack-protector-all -mfpu=neon' --extra-ldflags='-L/Users/Brian1/development/ffmpeg-android/toolchain-android/lib -Wl,-z,relro -Wl,-z,now -pie' --extra-libs=-lm --extra-cxxflags=
07-14 22:30:35.963: D/ffmpeg(30354):   libavutil      54.  7.100 / 54.  7.100
07-14 22:30:35.963: D/ffmpeg(30354):   libavcodec     56.  1.100 / 56.  1.100
07-14 22:30:35.963: D/ffmpeg(30354):   libavformat    56.  4.101 / 56.  4.101
07-14 22:30:35.963: D/ffmpeg(30354):   libavdevice    56.  0.100 / 56.  0.100
07-14 22:30:35.963: D/ffmpeg(30354):   libavfilter     5.  1.100 /  5.  1.100
07-14 22:30:35.963: D/ffmpeg(30354):   libswscale      3.  0.100 /  3.  0.100
07-14 22:30:35.963: D/ffmpeg(30354):   libswresample   1.  1.100 /  1.  1.100
07-14 22:30:35.963: D/ffmpeg(30354):   libpostproc    53.  0.100 / 53.  0.100
07-14 22:30:35.963: D/ffmpeg(30354): Input #0, mov,mp4,m4a,3gp,3g2,mj2, from '/data/data/com.myapp.app/cache:temp/i7h4ajm0nim1mbcnrqotvrhhsc.mp4':
07-14 22:30:35.963: D/ffmpeg(30354):   Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):     major_brand     : mp42
07-14 22:30:35.963: D/ffmpeg(30354):     minor_version   : 0
07-14 22:30:35.963: D/ffmpeg(30354):     compatible_brands: isommp42
07-14 22:30:35.963: D/ffmpeg(30354):     creation_time   : 2015-07-15 05:30:32
07-14 22:30:35.963: D/ffmpeg(30354):   Duration: 00:00:02.75, start: 0.000000, bitrate: 9315 kb/s
07-14 22:30:35.963: D/ffmpeg(30354):     Stream #0:0(eng): Video: h264 (avc1 / 0x31637661), yuv420p, 960x720, 10062 kb/s, 29.97 fps, 29.97 tbr, 90k tbn, 180k tbc (default)
07-14 22:30:35.963: D/ffmpeg(30354):     Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):       rotate          : 90
07-14 22:30:35.963: D/ffmpeg(30354):       creation_time   : 2015-07-15 05:30:32
07-14 22:30:35.963: D/ffmpeg(30354):       handler_name    : VideoHandle
07-14 22:30:35.963: D/ffmpeg(30354):     Side data:
07-14 22:30:35.963: D/ffmpeg(30354):       displaymatrix: rotation of -90.00 degrees
07-14 22:30:35.963: D/ffmpeg(30354):     Stream #0:1(eng): Audio: aac (mp4a / 0x6134706D), 48000 Hz, stereo, fltp, 151 kb/s (default)
07-14 22:30:35.963: D/ffmpeg(30354):     Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):       creation_time   : 2015-07-15 05:30:32
07-14 22:30:35.963: D/ffmpeg(30354):       handler_name    : SoundHandle
07-14 22:30:35.963: D/ffmpeg(30354): [libx264 @ 0xb6808800] using SAR=4/3
07-14 22:30:35.963: D/ffmpeg(30354): [libx264 @ 0xb6808800] using cpu capabilities: none!
07-14 22:30:35.963: D/ffmpeg(30354): [libx264 @ 0xb6808800] profile Constrained Baseline, level 3.1
07-14 22:30:35.963: D/ffmpeg(30354): [adts @ 0xb685b000] Using AVStream.codec.time_base as a timebase hint to the muxer is deprecated. Set AVStream.time_base instead.
07-14 22:30:35.963: D/ffmpeg(30354): Output #0, mpegts, to '/data/data/com.myapp.app/cache:temp/p1t3bhs0oa3lpqa67g5i9ninm9.ts':
07-14 22:30:35.963: D/ffmpeg(30354):   Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):     major_brand     : mp42
07-14 22:30:35.963: D/ffmpeg(30354):     minor_version   : 0
07-14 22:30:35.963: D/ffmpeg(30354):     compatible_brands: isommp42
07-14 22:30:35.963: D/ffmpeg(30354):     encoder         : Lavf56.4.101
07-14 22:30:35.963: D/ffmpeg(30354):     Stream #0:0(eng): Video: h264 (libx264), yuv420p, 720x960 [SAR 4:3 DAR 1:1], q=-1--1, 29.97 fps, 90k tbn, 29.97 tbc (default)
07-14 22:30:35.963: D/ffmpeg(30354):     Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):       handler_name    : VideoHandle
07-14 22:30:35.963: D/ffmpeg(30354):       creation_time   : 2015-07-15 05:30:32
07-14 22:30:35.963: D/ffmpeg(30354):       rotate          : 0
07-14 22:30:35.963: D/ffmpeg(30354):       encoder         : Lavc56.1.100 libx264
07-14 22:30:35.963: D/ffmpeg(30354):     Stream #0:1(eng): Audio: aac (mp4a / 0x6134706D), 48000 Hz, stereo, 151 kb/s (default)
07-14 22:30:35.963: D/ffmpeg(30354):     Metadata:
07-14 22:30:35.963: D/ffmpeg(30354):       creation_time   : 2015-07-15 05:30:32
07-14 22:30:35.963: D/ffmpeg(30354):       handler_name    : SoundHandle
07-14 22:30:35.963: D/ffmpeg(30354): Stream mapping:
07-14 22:30:35.963: D/ffmpeg(30354):   Stream #0:0 -> #0:0 (h264 (native) -> h264 (libx264))
07-14 22:30:35.963: D/ffmpeg(30354):   Stream #0:1 -> #0:1 (copy)
07-14 22:30:35.963: D/ffmpeg(30354): Press [q] to stop, [?] for help
07-14 22:30:35.963: D/ffmpeg(30354): frame=   17 fps=0.0 q=27.0 size=       0kB time=00:00:00.36 bitrate=   0.0kbits/s    
07-14 22:30:35.963: D/ffmpeg(30354): frame=   33 fps= 32 q=27.0 size=     164kB time=00:00:01.15 bitrate=1163.1kbits/s    
07-14 22:30:35.963: D/ffmpeg(30354): frame=   46 fps= 30 q=29.0 size=     213kB time=00:00:01.33 b

Answer 1

You can try this (takes care of cropping AND downsizing)...

ffmpeg -i input.file -s 480x480 -vf crop=480:480,setdar=1:1,setsar=1:1 output.mp4

-s will set scale (video canvas area)
crop=480:480 will crop from centre.. if you need from specific use: crop=480:480:pos-X:pos-Y
setdar will set Display Aspect Ratio
setsar will set Sample Aspect Ratio

Results: (screen grabbed MP4 stills via MPC-Home Cinema)